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Information about the selected riboswitch displayed below

RiboSwitch_ID:

AB17978

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RiboSwitch type

FMN type switch

Bacteria strain target

Acinetobacter baymannii ATCC 17978

Length of Switch in nucleotides

151

Sequence

CATCGCTTCAGGGCGGGGTGTAATTCCCCACCGGTGGTAAAGTTAATTTTTATTGTTAAATTAACAAGCCCACGAGCTTAAATTATGTAATTTGAGCAGATTTGGTGAAACTCCAAAGCCGCGGTATAGTCCGGATGAAAGAAGACGACG

Above is displayed the nucleotide sequence of the Acinetobacter baymannii ATCC 17978, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 46 nt. 2) Cytosine(C) in the sequence= 28 nt. 3) Guanine(G) in the sequence= 37 nt. 4) Thiamine(T) in the sequence= 40 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 151 nt. 8) CG percentage of the sequence= 43.05% 9) *Melting temperature of the DNA based on the Wallace formula= 78.10oC 10) The entered DNA sequence(5-3) is-151 nt.: CATCGCTTCAGGGCGGGGTGTAATTCCCCACCGGTGGTAAAGTTAATTTTTAttgttaaattaacAAGCCCACGAGCTTAAATTATGTAATTTGAGCAGATTTGGTGAAACTCCAAAGCCGACGGTATAGTCCGGATGAAAGAAGACGACG 11) The complementary(Com) sequence(3-5) is-151 nt.: GTAGCGAAGTCCCGCCCCACATTAAGGGGTGGCCACCATTTCAATTAAAAATaacaatttaattgTTCGGGTGCTCGAATTTAATACATTAAACTCGTCTAAACCACTTTGAGGTTTCGGCTGCCATATCAGGCCTACTTTCTTCTGCTGC 12) The reverse(Rev) sequence(3-5) is-151 nt.: GCAGCAGAAGAAAGTAGGCCTGATATGGCAGCCGAAACCTCAAAGTGGTTTAGACGAGTTTAATGTATTAAATTCGAGCACCCGAAcaattaaattgttATTTTTAATTGAAATGGTGGCCACCCCTTAATGTGGGGCGGGACTTCGCTAC 13) The RevCom sequence(5-3) is-151 nt.: CGTCGTCTTCTTTCATCCGGACTATACCGTCGGCTTTGGAGTTTCACCAAATCTGCTCAAATTACATAATTTAAGCTCGTGGGCTTgttaatttaacaaTAAAAATTAACTTTACCACCGGTGGGGAATTACACCCCGCCCTGAAGCGATG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-86 nt.: CATCGCTTCAGGGCGGGGTGTAATTCCCCACCGGTGGTAAAGTTAATTTTTAttgttaaattaacAAGCCCACGAGCTTAAATTAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-86 nt.: CGTCGTCTTCTTTCATCCGGACTATACCGTCGGCTTTGGAGTTTCACCAAATCTGCTCAAATTACATAATTTAAGCTCGTGGGCTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Acinetobacter baymannii ATCC 17978, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Acinetobacter baymannii ATCC 17978, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -44.40 kcal/mol is given below at structure (A). The free energy of the thermodynamic ensemble is -45.63 kcal/mol. The frequency of the MFE structure in the ensemble is 13.64 %. The ensemble diversity is 7.59. The centroid secondary structure in dot-bracket notation with a minimum free energy of -40.40 kcal/mol is given below in graph (B)

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Acinetobacter baymannii ATCC 17978, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Acinetobacter baymannii ATCC 17978, FMN type switch.

Multiple alignment of the FMN type switches

Below is presented the sequences alignment of all the FMN type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the FMN type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the FMN riboswitches and shorter motifs based on the general one: 1) N{0,4}RTYYTCRGGGCRGGGTGN?AATTCCCN?ACCGGCGGTRN{0,14}AGYCCGCGARCN{0,17}RRY?GATYYGGTGN?RAYTCCRRRRCCGACRGTAN?AGTCYGGATGRRAGARRRN?RN{0,3} 2) RTYYTCRGGGCRGGGTGN 3) AGTCYGGATGRRAGARRR Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

Key: N{0,4} = No, or up to 4 nucleotides can be present at the N position. N? = No or 1 nucleotide can be present at the N position.
The IUB ambiguity codes are : R = (G or A), Y = (C or T), M = (A or C), K = (G or T), S = (G or C), W = (A or T), B = (C or G or T), D = (A or G or T), H = (A or C or T), V = (A or C or G), N = (A or C or G or T)*

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

The table displays known human pathogenic bacteria bearing the FMN type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BA6153

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RiboSwitch type

FMN type switch

Bacteria strain target

Bacillus anthracis str Western North America

Length of Switch in nucleotides

140

Sequence

GTCTATCTTCGGGGCAGGGTGAAAATCCCGACCGGCGGTGATGAACTATTTATGATTTTGTCTAAGCCCGCGAGCCGTTAAGGCAGGATTTGGTGTGATTCCAAAGCCGACAGTATAGTCTGGATGGGAGAAGATGGAG

Above is displayed the nucleotide sequence of the Bacillus anthracis str Western North America, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 25 nt. 3) Guanine(G) in the sequence= 45 nt. 4) Thiamine(T) in the sequence= 36 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 140 nt. 8) CG percentage of the sequence= 50.00% 9) *Melting temperature of the DNA based on the Wallace formula= 80.60oC 10) The entered DNA sequence(5-3) is-140 nt.: GTCTATCTTCGGGGCAGGGTGAAAATCCCGACCGGCGGTGATGAACTATTTATgattttgttctAAGCCCGCGAGCCGTTAAGGCAGGATTTGGTGTGATTCCAAAGCCGACAGTATAGTCTGGATGGGAGAAGATGGAG 11) The complementary(Com) sequence(3-5) is-140 nt.: CAGATAGAAGCCCCGTCCCACTTTTAGGGCTGGCCGCCACTACTTGATAAATActaaaacaagaTTCGGGCGCTCGGCAATTCCGTCCTAAACCACACTAAGGTTTCGGCTGTCATATCAGACCTACCCTCTTCTACCTC 12) The reverse(Rev) sequence(3-5) is-140 nt.: GAGGTAGAAGAGGGTAGGTCTGATATGACAGCCGAAACCTTAGTGTGGTTTAGGACGGAATTGCCGAGCGCCCGAAtcttgttttagTATTTATCAAGTAGTGGCGGCCAGCCCTAAAAGTGGGACGGGGCTTCTATCTG 13) The RevCom sequence(5-3) is-140 nt.: CTCCATCTTCTCCCATCCAGACTATACTGTCGGCTTTGGAATCACACCAAATCCTGCCTTAACGGCTCGCGGGCTTagaacaaaatcATAAATAGTTCATCACCGCCGGTCGGGATTTTCACCCTGCCCCGAAGATAGAC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-80 nt.: GTCTATCTTCGGGGCAGGGTGAAAATCCCGACCGGCGGTGATGAACTATTTATgattttgttctAAGCCCGCGAGCCGTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-80 nt.: CTCCATCTTCTCCCATCCAGACTATACTGTCGGCTTTGGAATCACACCAAATCCTGCCTTAACGGCTCGCGGGCTTagaa

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis str Western North America, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis str Western North America, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -42.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -44.39 kcal/mol. The frequency of the MFE structure in the ensemble is 2.06 %. The ensemble diversity is 16.16 . You may look at the dot plot containing the base pair probabilities The centroid secondary structure in dot-bracket notation with a minimum free energy of -39.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis str Western North America, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis str Western North America, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

BS46789

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RiboSwitch type

FMN type switch

Bacteria strain target

Bacillus subtilis_1

Length of Switch in nucleotides

145

Sequence

TTGTATCTTCGGGGCAGGGTGGAAATCCCGACCGGCGGTAGTAAAGCACATTTGCTTTAGAGCCCGTGACCCGTGTGCATAAGCACGCGGTGGATTCAGTTTAAGCTGAAGCCGACAGTGAAAGTCTGGATGGGAGAAGGATGAT

Above is displayed the nucleotide sequence of the Bacillus subtilis_1, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 28 nt. 3) Guanine(G) in the sequence= 48 nt. 4) Thiamine(T) in the sequence= 33 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 145 nt. 8) CG percentage of the sequence= 52.41% 9) *Melting temperature of the DNA based on the Wallace formula= 81.75oC 10) The entered DNA sequence(5-3) is-145 nt.: TTGTATCTTCGGGGCAGGGTGGAAATCCCGACCGGCGGTAGTAAAGCACATTTgctttaGAGCCCGTGACCCGTGTGCATAAGCACGCGGTGGATTCAGTTTAAGCTGAAGCCGACAGtGAAAGTCTGGATGGGAGAAGGATGAT 11) The complementary(Com) sequence(3-5) is-145 nt.: AACATAGAAGCCCCGTCCCACCTTTAGGGCTGGCCGCCATCATTTCGTGTAAAcgaaatCTCGGGCACTGGGCACACGTATTCGTGCGCCACCTAAGTCAAATTCGACTTCGGCTGTCaCTTTCAGACCTACCCTCTTCCTACTA 12) The reverse(Rev) sequence(3-5) is-145 nt.: TAGTAGGAAGAGGGTAGGTCTGAAAGtGACAGCCGAAGTCGAATTTGACTTAGGTGGCGCACGAATACGTGTGCCCAGTGCCCGAGatttcgTTTACACGAAATGATGGCGGCCAGCCCTAAAGGTGGGACGGGGCTTCTATGTT 13) The RevCom sequence(5-3) is-145 nt.: ATCATCCTTCTCCCATCCAGACTTTCaCTGTCGGCTTCAGCTTAAACTGAATCCACCGCGTGCTTATGCACACGGGTCACGGGCTCtaaagcAAATGTGCTTTACTACCGCCGGTCGGGATTTCCACCCTGCCCCGAAGATACAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-83 nt.: TTGTATCTTCGGGGCAGGGTGGAAATCCCGACCGGCGGTAGTAAAGCACATTTgctttaGAGCCCGTGACCCGTGTGCATAAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-83 nt.: ATCATCCTTCTCCCATCCAGACTTTCaCTGTCGGCTTCAGCTTAAACTGAATCCACCGCGTGCTTATGCACACGGGTCACGGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis_1, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis_1, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -48.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -52.48 kcal/mol. The frequency of the MFE structure in the ensemble is 0.30 %. The ensemble diversity is 28.48 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -33.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis_1, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis_1, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

BS176482

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RiboSwitch type

FMN type switch

Bacteria strain target

Bacillus subtilis_2

Length of Switch in nucleotides

145

Sequence

TGTATCCTTCGGGGCAGGGTGGAAATCCCGACCGGCGGTAGTAAAGCACATTTGCTTTAGAGCCCGTGACCCGTGTGCATAAGCACGCGGTGGATTCAGTTTAAGCTGAAGCCGACAGTGAAAGTCTGGATGGGAGAAGGATGAT

Above is displayed the nucleotide sequence of the Bacillus subtilis_2, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 29 nt. 3) Guanine(G) in the sequence= 48 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 145 nt. 8) CG percentage of the sequence= 53.10% 9) *Melting temperature of the DNA based on the Wallace formula= 82.04oC 10) The entered DNA sequence(5-3) is-145 nt.: TGTATCCTTCGGGGCAGGGTGGAAATCCCGACCGGCGGTAGTAAAGCACATTTgctttaGAGCCCGTGACCCGTGTGCATAAGCACGCGGTGGATTCAGTTTAAGCTGAAGCCGACAGtGAAAGTCTGGATGGGAGAAGGATGAT 11) The complementary(Com) sequence(3-5) is-145 nt.: ACATAGGAAGCCCCGTCCCACCTTTAGGGCTGGCCGCCATCATTTCGTGTAAAcgaaatCTCGGGCACTGGGCACACGTATTCGTGCGCCACCTAAGTCAAATTCGACTTCGGCTGTCaCTTTCAGACCTACCCTCTTCCTACTA 12) The reverse(Rev) sequence(3-5) is-145 nt.: TAGTAGGAAGAGGGTAGGTCTGAAAGtGACAGCCGAAGTCGAATTTGACTTAGGTGGCGCACGAATACGTGTGCCCAGTGCCCGAGatttcgTTTACACGAAATGATGGCGGCCAGCCCTAAAGGTGGGACGGGGCTTCCTATGT 13) The RevCom sequence(5-3) is-145 nt.: ATCATCCTTCTCCCATCCAGACTTTCaCTGTCGGCTTCAGCTTAAACTGAATCCACCGCGTGCTTATGCACACGGGTCACGGGCTCtaaagcAAATGTGCTTTACTACCGCCGGTCGGGATTTCCACCCTGCCCCGAAGGATACA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-83 nt.: TGTATCCTTCGGGGCAGGGTGGAAATCCCGACCGGCGGTAGTAAAGCACATTTgctttaGAGCCCGTGACCCGTGTGCATAAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis_2, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis_2, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -57.31 kcal/mol. The frequency of the MFE structure in the ensemble is 0.76 %. The ensemble diversity is 17.29 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -49.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis_2, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis_2, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

BS745564

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RiboSwitch type

FMN type switch

Bacteria strain target

Bacillus subtilis_3

Length of Switch in nucleotides

135

Sequence

ATCAATCTTCGGGGCAGGGTGAAATTCCCTACCGGCGGTGATGAGCCAATGGCTCTAAGCCCGCGAGCTGTCTTTACAGCAGGATTCGGTGAGATTCCGGAGCCGACAGTACAGTCTGGATGGGAGAAGATGGAG

Above is displayed the nucleotide sequence of the Bacillus subtilis_3, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 30 nt. 3) Guanine(G) in the sequence= 45 nt. 4) Thiamine(T) in the sequence= 28 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 135 nt. 8) CG percentage of the sequence= 55.56% 9) *Melting temperature of the DNA based on the Wallace formula= 82.70oC 10) The entered DNA sequence(5-3) is-135 nt.: ATCAATCTTCGGGGCAGGGTGAAATTCCCTACCGGCGGTGATGAGCCAATGGCtctAAGCCCGCGAGCTGTCTTTACAGCAGGATTCGGTGAGATTCCGGAGCCGACAGTACAGTCTGGATGGGAGAAGATGGAG 11) The complementary(Com) sequence(3-5) is-135 nt.: TAGTTAGAAGCCCCGTCCCACTTTAAGGGATGGCCGCCACTACTCGGTTACCGagaTTCGGGCGCTCGACAGAAATGTCGTCCTAAGCCACTCTAAGGCCTCGGCTGTCATGTCAGACCTACCCTCTTCTACCTC 12) The reverse(Rev) sequence(3-5) is-135 nt.: GAGGTAGAAGAGGGTAGGTCTGACATGACAGCCGAGGCCTTAGAGTGGCTTAGGACGACATTTCTGTCGAGCGCCCGAAtctCGGTAACCGAGTAGTGGCGGCCATCCCTTAAAGTGGGACGGGGCTTCTAACTA 13) The RevCom sequence(5-3) is-135 nt.: CTCCATCTTCTCCCATCCAGACTGTACTGTCGGCTCCGGAATCTCACCGAATCCTGCTGTAAAGACAGCTCGCGGGCTTagaGCCATTGGCTCATCACCGCCGGTAGGGAATTTCACCCTGCCCCGAAGATTGAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-78 nt.: ATCAATCTTCGGGGCAGGGTGAAATTCCCTACCGGCGGTGATGAGCCAATGGCtctAAGCCCGCGAGCTGTCTTTACA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-78 nt.: CTCCATCTTCTCCCATCCAGACTGTACTGTCGGCTCCGGAATCTCACCGAATCCTGCTGTAAAGACAGCTCGCGGGCT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis_3, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis_3, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -45.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -48.09 kcal/mol. The frequency of the MFE structure in the ensemble is 1.27 %. The ensemble diversity is 17.61 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -42.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis_3, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis_3, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

BC23365

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RiboSwitch type

FMN type switch

Bacteria strain target

Brucella canis ATCC 23365

Length of Switch in nucleotides

164

Sequence

GCTTGTTCTCGGGGCGGGGTGAAACTCCCCACCGGCGGTATGAAAAGCAATTTTCAAGCCCGCGAGCGCCTGAAATGGAAGCCGATTCGCATGCCATTTCAGGGTCAGCAGATCCGGTGAGATGCCGGAGCCGACGGTTAAAGTCCGGATGGAAGAGAGCGAAT

Above is displayed the nucleotide sequence of the Brucella canis ATCC 23365, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 40 nt. 2) Cytosine(C) in the sequence= 40 nt. 3) Guanine(G) in the sequence= 54 nt. 4) Thiamine(T) in the sequence= 30 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 164 nt. 8) CG percentage of the sequence= 57.32% 9) *Melting temperature of the DNA based on the Wallace formula= 84.30oC 10) The entered DNA sequence(5-3) is-164 nt.: GCTTGTTCTCGGGGCGGGGTGAAACTCCCCACCGGCGGTATGAAAAGCAATTTtcAAGCCCGCGAGCGCCTGAAAtggaagccgattcgcatgccaTTTCAGGGTCAGCAGATCCGGTGAGATGCCGGAGCCGACGGtTAAAGTCCGGATGGAAGAGAGCGAAT 11) The complementary(Com) sequence(3-5) is-164 nt.: CGAACAAGAGCCCCGCCCCACTTTGAGGGGTGGCCGCCATACTTTTCGTTAAAagTTCGGGCGCTCGCGGACTTTaccttcggctaagcgtacggtAAAGTCCCAGTCGTCTAGGCCACTCTACGGCCTCGGCTGCCaATTTCAGGCCTACCTTCTCTCGCTTA 12) The reverse(Rev) sequence(3-5) is-164 nt.: TAAGCGAGAGAAGGTAGGCCTGAAATtGGCAGCCGAGGCCGTAGAGTGGCCTAGACGACTGGGACTTTaccgtacgcttagccgaaggtAAAGTCCGCGAGCGCCCGAActTTTAACGAAAAGTATGGCGGCCACCCCTCAAAGTGGGGCGGGGCTCTTGTTCG 13) The RevCom sequence(5-3) is-164 nt.: ATTCGCTCTCTTCCATCCGGACTTTAaCCGTCGGCTCCGGCATCTCACCGGATCTGCTGACCCTGAAAtggcatgcgaatcggcttccaTTTCAGGCGCTCGCGGGCTTgaAAATTGCTTTTCATACCGCCGGTGGGGAGTTTCACCCCGCCCCGAGAACAAGC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-92 nt.: GCTTGTTCTCGGGGCGGGGTGAAACTCCCCACCGGCGGTATGAAAAGCAATTTtcAAGCCCGCGAGCGCCTGAAAtggaagccgattcgcat 15) The RevCom sequence(5-3) to order a 10nt overlapping region-92 nt.: ATTCGCTCTCTTCCATCCGGACTTTAaCCGTCGGCTCCGGCATCTCACCGGATCTGCTGACCCTGAAAtggcatgcgaatcggcttccaTTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Brucella canis ATCC 23365, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Brucella canis ATCC 23365, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -64.70 kcal/mol is given below. at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -66.87 kcal/mol. The frequency of the MFE structure in the ensemble is 2.94 %. The ensemble diversity is 33.53 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -52.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Brucella canis ATCC 23365, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Brucella canis ATCC 23365, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

CB23345

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RiboSwitch type

FMN type switch

Bacteria strain target

Clostridium botulinum C str_Eklund

Length of Switch in nucleotides

123

Sequence

TAGTATCTTCAGGGCAGGGTGTAATTCCCGACCGGCGGTTAAAGTCCGCGAGCTTTATTTTTATATGGCTGATTTGGTGAAACTCCAAAACCGACAGTAAAGTCTGGATGAGAGAAGGTATAG

Above is displayed the nucleotide sequence of the Clostridium botulinum C str_Eklund , FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 34 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 123 nt. 8) CG percentage of the sequence= 44.72% 9) *Melting temperature of the DNA based on the Wallace formula= 77.77oC 10) The entered DNA sequence(5-3) is-123 nt.: TAGTATCTTCAGGGCAGGGTGTAATTCCCGACCGGCGGTTAAAGTCCGCGAGCTTTATTTTTATATGGCTGATTTGGTGAAACTCCAAAACCGACAGTAAAGTCTGGATGAGAGAAGGTATAG 11) The complementary(Com) sequence(3-5) is-123 nt.: ATCATAGAAGTCCCGTCCCACATTAAGGGCTGGCCGCCAATTTCAGGCGCTCGAAATAAAAATATACCGACTAAACCACTTTGAGGTTTTGGCTGTCATTTCAGACCTACTCTCTTCCATATC 12) The reverse(Rev) sequence(3-5) is-123 nt.: GATATGGAAGAGAGTAGGTCTGAAATGACAGCCAAAACCTCAAAGTGGTTTAGTCGGTATATTTTTATTTCGAGCGCCTGAAATTGGCGGCCAGCCCTTAATGTGGGACGGGACTTCTATGAT 13) The RevCom sequence(5-3) is-123 nt.: CTATACCTTCTCTCATCCAGACTTTACTGTCGGTTTTGGAGTTTCACCAAATCAGCCATATAAAAATAAAGCTCGCGGACTTTAACCGCCGGTCGGGAATTACACCCTGCCCTGAAGATACTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-72 nt.: TAGTATCTTCAGGGCAGGGTGTAATTCCCGACCGGCGGTTAAAGTCCGCGAGCTTTATTTTTATATGGCTGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-72 nt.: CTATACCTTCTCTCATCCAGACTTTACTGTCGGTTTTGGAGTTTCACCAAATCAGCCATATAAAAATAAAGC ?

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum C str_Eklund , FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum C str_Eklund , FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -34.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -34.92 kcal/mol. The frequency of the MFE structure in the ensemble is 26.24 %. The ensemble diversity is 7.64 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -34.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum C str_Eklund , FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum C str_Eklund , FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

CB23347

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RiboSwitch type

FMN type switch

Bacteria strain target

Clostridium botulinum A2 str_Kyoto

Length of Switch in nucleotides

117

Sequence

TTATATCTTCAGGGCGGGGTGTAATTCCCCACCGGCGGTAAAGCCCGCGAGCTATTTTTAGCATGATTCGGTTAAATTCCGAAGCCGACAGTAAAGTCTGGATGGAAGAAGATTATA

Above is displayed the nucleotide sequence of the Clostridium botulinum A2 str_Kyoto, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 31 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 117 nt. 8) CG percentage of the sequence= 46.15% 9) *Melting temperature of the DNA based on the Wallace formula= 78.08oC 10) The entered DNA sequence(5-3) is-117 nt.: TTATATCTTCAGGGCGGGGTGTAATTCCCCACCGGCGGTAAAGCCCGCGAGCTATTTTTAGCATGATTCGGTTAAATTCCGAAGCCGACAGTAAAGTCTGGATGGAAGAAGATTATA 11) The complementary(Com) sequence(3-5) is-117 nt.: AATATAGAAGTCCCGCCCCACATTAAGGGGTGGCCGCCATTTCGGGCGCTCGATAAAAATCGTACTAAGCCAATTTAAGGCTTCGGCTGTCATTTCAGACCTACCTTCTTCTAATAT 12) The reverse(Rev) sequence(3-5) is-117 nt.: ATATTAGAAGAAGGTAGGTCTGAAATGACAGCCGAAGCCTTAAATTGGCTTAGTACGATTTTTATCGAGCGCCCGAAATGGCGGCCACCCCTTAATGTGGGGCGGGACTTCTATATT 13) The RevCom sequence(5-3) is-117 nt.: TATAATCTTCTTCCATCCAGACTTTACTGTCGGCTTCGGAATTTAACCGAATCATGCTAAAAATAGCTCGCGGGCTTTACCGCCGGTGGGGAATTACACCCCGCCCTGAAGATATAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-69 nt.: TTATATCTTCAGGGCGGGGTGTAATTCCCCACCGGCGGTAAAGCCCGCGAGCTATTTTTAGCATGATTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-69 nt.: TATAATCTTCTTCCATCCAGACTTTACTGTCGGCTTCGGAATTTAACCGAATCATGCTAAAAATAGCTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum A2 str_Kyoto, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum A2 str_Kyoto, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -36.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.43 kcal/mol. The frequency of the MFE structure in the ensemble is 8.35 %. The ensemble diversity is 13.22 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum A2 str_Kyoto, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum A2 str_Kyoto, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

BL5262

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RiboSwitch type

FMN type switch

Bacteria strain target

Clostridium botulinum E4 str_BoNT_E_BL5262

Length of Switch in nucleotides

115

Sequence

ATATATCTTCAGGGCAGGGTGAAAATCCCTACTGGCGGTACAGCCCGCGAGCTATTTTAGA GATTCGGTGTAATTCCGAAGCCAACAGTATAGTCTGGATGAAAGAAGGTAACC

Above is displayed the nucleotide sequence of the Clostridium botulinum E4 str_BoNT_E_BL5262, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 30 nt. 4) Thiamine(T) in the sequence= 27 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 115 nt. 8) CG percentage of the sequence= 46.96% 9) *Melting temperature of the DNA based on the Wallace formula= 78.31oC 10) The entered DNA sequence(5-3) is-115 nt.: ATATATCTTCAGGGCAGGGTGAAAATCCCTACTGGCGGTACAGCCCGCGAGCTATTTTAGCAGATTCGGTGTAATTCCGAAGCCAACAGTATAGTCTGGATGAAAGAAGGTAACC 11) The complementary(Com) sequence(3-5) is-115 nt.: TATATAGAAGTCCCGTCCCACTTTTAGGGATGACCGCCATGTCGGGCGCTCGATAAAATCGTCTAAGCCACATTAAGGCTTCGGTTGTCATATCAGACCTACTTTCTTCCATTGG 12) The reverse(Rev) sequence(3-5) is-115 nt.: CCAATGGAAGAAAGTAGGTCTGATATGACAACCGAAGCCTTAATGTGGCTTAGACGATTTTATCGAGCGCCCGACATGGCGGTCATCCCTAAAAGTGGGACGGGACTTCTATATA 13) The RevCom sequence(5-3) is-115 nt.: GGTTACCTTCTTTCATCCAGACTATACTGTTGGCTTCGGAATTACACCGAATCTGCTAAAATAGCTCGCGGGCTGTACCGCCAGTAGGGATTTTCACCCTGCCCTGAAGATATAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-68 nt.: ATATATCTTCAGGGCAGGGTGAAAATCCCTACTGGCGGTACAGCCCGCGAGCTATTTTAGCAGATTCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-68 nt.: GGTTACCTTCTTTCATCCAGACTATACTGTTGGCTTCGGAATTACACCGAATCTGCTAAAATAGCTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum E4 str_BoNT_E_BL5262, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum E4 str_BoNT_E_BL5262, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -29.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -31.53 kcal/mol. The frequency of the MFE structure in the ensemble is 6.04 %. The ensemble diversity is 11.13 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -30.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum E4 str_BoNT_E_BL5262, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum E4 str_BoNT_E_BL5262, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

CL5263

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RiboSwitch type

FMN type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

122

Sequence

GAAGATCTTCGGGGCAGGGTGAAATTCCCTACCGGCGGTATAGCCCGCGAACTACTTAGGGGTTGATTTGGTGAGATTCCAAAGCCGACAGTAAAGTCTGGATGAGAGAAGATATTT

Above is displayed the nucleotide sequence of the Clostridium difficile, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 33 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 122 nt. 8) CG percentage of the sequence= 44.26% 9) *Melting temperature of the DNA based on the Wallace formula= 77.54oC 10) The entered DNA sequence(5-3) is-122 nt.: CTTAATCTTCGGGGTAGGGTGAAATTCCCAATCGGCGGTATAGCCCGCGAGCCAAGGTAAAACTTGGTTGATTTGGTTAAATTCCAAAGCCGACAGTAAAGTCTGGATGGAAGAAGATATTT 11) The complementary(Com) sequence(3-5) is-122 nt.: GAATTAGAAGCCCCATCCCACTTTAAGGGTTAGCCGCCATATCGGGCGCTCGGTTCCATTTTGAACCAACTAAACCAATTTAAGGTTTCGGCTGTCATTTCAGACCTACCTTCTTCTATAAA 12) The reverse(Rev) sequence(3-5) is-122 nt.: TTTATAGAAGAAGGTAGGTCTGAAATGACAGCCGAAACCTTAAATTGGTTTAGTTGGTTCAAAATGGAACCGAGCGCCCGATATGGCGGCTAACCCTTAAAGTGGGATGGGGCTTCTAATTC 13) The RevCom sequence(5-3) is-122 nt.: AAATATCTTCTTCCATCCAGACTTTACTGTCGGCTTTGGAATTTAACCAAATCAACCAAGTTTTACCTTGGCTCGCGGGCTATACCGCCGATTGGGAATTTCACCCTACCCCGAAGATTAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-71 nt.: CTTAATCTTCGGGGTAGGGTGAAATTCCCAATCGGCGGTATAGCCCGCGAGCCAAGGTAAAACTTGGTTGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-71 nt.: AAATATCTTCTTCCATCCAGACTTTACTGTCGGCTTTGGAATTTAACCAAATCAACCAAGTTTTACCTTGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -35.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -37.10 kcal/mol. The frequency of the MFE structure in the ensemble is 10.25 %. The ensemble diversity is 18.44 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -31.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

QCD32g58

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RiboSwitch type

FMN type switch

Bacteria strain target

Clostridium difficile QCD32g58

Length of Switch in nucleotides

118

Sequence

GAAGATCTTCGGGGCAGGGTGAAATTCCCTACCGGCGGTATAGCCCGCGAACTACTTAGGGGTTGATTTGGTGAGATTCCAAAGCCGACAGTAAAGTCTGGATGAGAGAAGATATTT

Above is displayed the nucleotide sequence of the Clostridium difficile QCD32g58, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 36 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 118 nt. 8) CG percentage of the sequence= 48.31% 9) *Melting temperature of the DNA based on the Wallace formula= 79.01oC 10) The entered DNA sequence(5-3) is-118 nt.: GAAGATCTTCGGGGCAGGGTGAAATTCCCTACCGGCGGTATAGCCCGCGAACTACTTAGGTGGTTGATTTGGTGAGATTCCAAAGCCGACAGTAAAGTCTGGATGAGAGAAGATATTT 11) The complementary(Com) sequence(3-5) is-118 nt.: CTTCTAGAAGCCCCGTCCCACTTTAAGGGATGGCCGCCATATCGGGCGCTTGATGAATCCACCAACTAAACCACTCTAAGGTTTCGGCTGTCATTTCAGACCTACTCTCTTCTATAAA 12) The reverse(Rev) sequence(3-5) is-118 nt.: TTTATAGAAGAGAGTAGGTCTGAAATGACAGCCGAAACCTTAGAGTGGTTTAGTTGGTGGATTCATCAAGCGCCCGATATGGCGGCCATCCCTTAAAGTGGGACGGGGCTTCTAGAAG 13) The RevCom sequence(5-3) is-118 nt.: AAATATCTTCTCTCATCCAGACTTTACTGTCGGCTTTGGAATCTCACCAAATCAACCACCTAAGTAGTTCGCGGGCTATACCGCCGGTAGGGAATTTCACCCTGCCCCGAAGATCTTC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-69 nt.: GAAGATCTTCGGGGCAGGGTGAAATTCCCTACCGGCGGTATAGCCCGCGAACTACTTAGGTGGTTGATT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-69 nt.: AAATATCTTCTCTCATCCAGACTTTACTGTCGGCTTTGGAATCTCACCAAATCAACCACCTAAGTAGTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile QCD32g58, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile QCD32g58, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -33.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -35.13 kcal/mol. The frequency of the MFE structure in the ensemble is 13.62 %. The ensemble diversity is 10.03 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -33.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile QCD32g58, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile QCD32g58, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

F4969

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RiboSwitch type

FMN type switch

Bacteria strain target

Clostridium_perfringens CPE str_F4969

Length of Switch in nucleotides

118

Sequence

AAAAGTCTTCAGGGCGGGGTGTAAGTCCCCACCGGCGGTAAAGCCCGCGAGCTAGTTTTTAGCATGATTCGGTGAAATTCCGAGGCCGACAGTATAGTCTGGATGAAAGAAGATGAGT

Above is displayed the nucleotide sequence of the Clostridium_perfringens CPE str_F4969, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 37 nt. 4) Thiamine(T) in the sequence= 26 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 118 nt. 8) CG percentage of the sequence= 50.85% 9) *Melting temperature of the DNA based on the Wallace formula= 80.05oC 10) The entered DNA sequence(5-3) is-118 nt.: AAAAGTCTTCAGGGCGGGGTGTAAGTCCCCACCGGCGGTAAAGCCCGCGAGCTAGTTTTTAGCATGATTCGGTGAAATTCCGAGGCCGACAGTATAGTCTGGATGAAAGAAGATGAGT 11) The complementary(Com) sequence(3-5) is-118 nt.: TTTTCAGAAGTCCCGCCCCACATTCAGGGGTGGCCGCCATTTCGGGCGCTCGATCAAAAATCGTACTAAGCCACTTTAAGGCTCCGGCTGTCATATCAGACCTACTTTCTTCTACTCA 12) The reverse(Rev) sequence(3-5) is-118 nt.: TGAGTAGAAGAAAGTAGGTCTGATATGACAGCCGGAGCCTTAAAGTGGCTTAGTACGATTTTTGATCGAGCGCCCGAAATGGCGGCCACCCCTGAATGTGGGGCGGGACTTCTGAAAA 13) The RevCom sequence(5-3) is-118 nt.: ACTCATCTTCTTTCATCCAGACTATACTGTCGGCCTCGGAATTTCACCGAATCATGCTAAAAACTAGCTCGCGGGCTTTACCGCCGGTGGGGACTTACACCCCGCCCTGAAGACTTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-69 nt.: AAAAGTCTTCAGGGCGGGGTGTAAGTCCCCACCGGCGGTAAAGCCCGCGAGCTAGTTTTTAGCATGATT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-69 nt.: ACTCATCTTCTTTCATCCAGACTATACTGTCGGCCTCGGAATTTCACCGAATCATGCTAAAAACTAGCT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium_perfringens CPE str_F4969, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium_perfringens CPE str_F4969, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -35.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -36.66 kcal/mol. The frequency of the MFE structure in the ensemble is 11.09 %. The ensemble diversity is 10.01 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -35.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium_perfringens CPE str_F4969, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium_perfringens CPE str_F4969, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

CTE88

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RiboSwitch type

FMN type switch

Bacteria strain target

Clostridium tetani_E88

Length of Switch in nucleotides

115

Sequence

AAATATCTTCAGGGCGGGGTGTAATTCCCCACCGGCGGTATAGCCCGCGAGCCGCAAGGCATGATTCGGTGTAACTCCGAAGCCGACAGTAAAGTCTGGATGAAAGAAGGTATAA

Above is displayed the nucleotide sequence of the Clostridium tetani_E88, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 26 nt. 3) Guanine(G) in the sequence= 34 nt. 4) Thiamine(T) in the sequence= 22 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 115 nt. 8) CG percentage of the sequence= 52.17% 9) *Melting temperature of the DNA based on the Wallace formula= 80.44oC 10) The entered DNA sequence(5-3) is-115 nt.: AAATATCTTCAGGGCGGGGTGTAATTCCCCACCGGCGGTATAGCCCGCGAGCCGCAAGGCATGATTCGGTGTAACTCCGAAGCCGACAGTAAAGTCTGGATGAAAGAAGGTATAA 11) The complementary(Com) sequence(3-5) is-115 nt.: TTTATAGAAGTCCCGCCCCACATTAAGGGGTGGCCGCCATATCGGGCGCTCGGCGTTCCGTACTAAGCCACATTGAGGCTTCGGCTGTCATTTCAGACCTACTTTCTTCCATATT 12) The reverse(Rev) sequence(3-5) is-115 nt.: AATATGGAAGAAAGTAGGTCTGAAATGACAGCCGAAGCCTCAATGTGGCTTAGTACGGAACGCCGAGCGCCCGATATGGCGGCCACCCCTTAATGTGGGGCGGGACTTCTATAAA 13) The RevCom sequence(5-3) is-115 nt.: TTATACCTTCTTTCATCCAGACTTTACTGTCGGCTTCGGAGTTACACCGAATCATGCCTTGCGGCTCGCGGGCTATACCGCCGGTGGGGAATTACACCCCGCCCTGAAGATATTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-68 nt.: AAATATCTTCAGGGCGGGGTGTAATTCCCCACCGGCGGTATAGCCCGCGAGCCGCAAGGCATGATTCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-68 nt.: TTATACCTTCTTTCATCCAGACTTTACTGTCGGCTTCGGAGTTACACCGAATCATGCCTTGCGGCTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani_E88, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani_E88, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -39.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -40.34 kcal/mol. The frequency of the MFE structure in the ensemble is 30.28 %. The ensemble diversity is 10.83 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -39.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani_E88, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani_E88, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

EsCOl352

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RiboSwitch type

FMN type switch

Bacteria strain target

Escherichia coli

Length of Switch in nucleotides

148

Sequence

GCTTATTCTCAGGGCGGGGCGAAATTCCCCACCGGCGGTAAATCAACTCAGTTGAAAGCCGCGAGCGCTTTGGGTGCGAACTCAAAGGACAGCAGATCCGGTGTAATTCCGGGGCCGACGGTAGAGTCCGGATGGGAGAGAGTAACG

Above is displayed the nucleotide sequence of the Escherichia coli, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 35 nt. 3) Guanine(G) in the sequence= 50 nt. 4) Thiamine(T) in the sequence= 27 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 148 nt. 8) CG percentage of the sequence= 57.43% 9) *Melting temperature of the DNA based on the Wallace formula= 83.90oC 10) The entered DNA sequence(5-3) is-148 nt.: GCTTATTCTCAGGGCGGGGCGAAATTCCCCACCGGCGGTAAATCAACTCAGTTgaAAGCCGCGAGCGCTTTGGGtgcgaaCTCAAAGGACAGCAGATCCGGTGTAATTCCGGGGCCGACGGtTAGAGTCCGGATGGGAGAGAGTAACG 11) The complementary(Com) sequence(3-5) is-148 nt.: CGAATAAGAGTCCCGCCCCGCTTTAAGGGGTGGCCGCCATTTAGTTGAGTCAActTTCGGCGCTCGCGAAACCCacgcttGAGTTTCCTGTCGTCTAGGCCACATTAAGGCCCCGGCTGCCaATCTCAGGCCTACCCTCTCTCATTGC 12) The reverse(Rev) sequence(3-5) is-148 nt.: GCAATGAGAGAGGGTAGGCCTGAGATtGGCAGCCGGGGCCTTAATGTGGCCTAGACGACAGGAAACTCaagcgtGGGTTTCGCGAGCGCCGAAagTTGACTCAACTAAATGGCGGCCACCCCTTAAAGCGGGGCGGGACTCTTATTCG 13) The RevCom sequence(5-3) is-148 nt.: CGTTACTCTCTCCCATCCGGACTCTAaCCGTCGGCCCCGGAATTACACCGGATCTGCTGTCCTTTGAGttcgcaCCCAAAGCGCTCGCGGCTTtcAACTGAGTTGATTTACCGCCGGTGGGGAATTTCGCCCCGCCCTGAGAATAAGC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-84 nt.: GCTTATTCTCAGGGCGGGGCGAAATTCCCCACCGGCGGTAAATCAACTCAGTTgaAAGCCGCGAGCGCTTTGGGtgcgaaCTCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-84 nt.: CGTTACTCTCTCCCATCCGGACTCTAaCCGTCGGCCCCGGAATTACACCGGATCTGCTGTCCTTTGAGttcgcaCCCAAAGCGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Escherichia coli, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Escherichia coli, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -51.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -53.34 kcal/mol. The frequency of the MFE structure in the ensemble is 9.60 %. The ensemble diversity is 21.24 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -51.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Escherichia coli, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Escherichia coli, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

H22121

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RiboSwitch type

FMN type switch

Bacteria strain target

Haemophilus influenzae_22121

Length of Switch in nucleotides

178

Sequence

TCGCATTCTCAGGGCAGGGTGAAATTCCCTACCGGTGGTAAAGCCCACGAGCGTTTAAAAGTGCGGTCAATTTTTGGCAAATTTTTCTTGCTAAATTGTCCTGATTTTCACTTTTAAAGTCAGCAGATTTGGTGAAATCCAAAGCCGACAGTAAAGTCTGGATGAAAGAGAATAAAA

Above is displayed the nucleotide sequence of the Haemophilus influenzae_22121, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 54 nt. 2) Cytosine(C) in the sequence= 32 nt. 3) Guanine(G) in the sequence= 40 nt. 4) Thiamine(T) in the sequence= 52 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 178 nt. 8) CG percentage of the sequence= 40.45% 9) *Melting temperature of the DNA based on the Wallace formula= 77.71oC 10) The entered DNA sequence(5-3) is-178 nt.: TCGCATTCTCAGGGCAGGGTGAAATTCCCTACCGGTGGTAAAGCCCACGAGCGTTTAAAAgtgcggtcaatttttggcaaatttttcttgctaaattgtcctgattttcacTTTTAAAGTCAGCAGATTTGGTGAAATTCCAAAGCCGACAGTAAAGTCTGGATGAAAGAGAATAAAA 11) The complementary(Com) sequence(3-5) is-178 nt.: AGCGTAAGAGTCCCGTCCCACTTTAAGGGATGGCCACCATTTCGGGTGCTCGCAAATTTTcacgccagttaaaaaccgtttaaaaagaacgatttaacaggactaaaagtgAAAATTTCAGTCGTCTAAACCACTTTAAGGTTTCGGCTGTCATTTCAGACCTACTTTCTCTTATTTT 12) The reverse(Rev) sequence(3-5) is-178 nt.: AAAATAAGAGAAAGTAGGTCTGAAATGACAGCCGAAACCTTAAAGTGGTTTAGACGACTGAAATTTTcacttttagtcctgttaaatcgttctttttaaacggtttttaactggcgtgAAAATTTGCGAGCACCCGAAATGGTGGCCATCCCTTAAAGTGGGACGGGACTCTTACGCT 13) The RevCom sequence(5-3) is-178 nt.: TTTTATTCTCTTTCATCCAGACTTTACTGTCGGCTTTGGAATTTCACCAAATCTGCTGACTTTAAAAgtgaaaatcaggacaatttagcaagaaaaatttgccaaaaattgaccgcacTTTTAAACGCTCGTGGGCTTTACCACCGGTAGGGAATTTCACCCTGCCCTGAGAATGCGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-99 nt.: TCGCATTCTCAGGGCAGGGTGAAATTCCCTACCGGTGGTAAAGCCCACGAGCGTTTAAAAgtgcggtcaatttttggcaaatttttcttgctaaattgt 15) The RevCom sequence(5-3) to order a 10nt overlapping region-99 nt.: TTTTATTCTCTTTCATCCAGACTTTACTGTCGGCTTTGGAATTTCACCAAATCTGCTGACTTTAAAAgtgaaaatcaggacaatttagcaagaaaaatt

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Haemophilus influenzae_22121, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Haemophilus influenzae_22121, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -49.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -50.12 kcal/mol. The frequency of the MFE structure in the ensemble is 16.34 %. The ensemble diversity is 17.99 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -49.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Haemophilus influenzae_22121, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Haemophilus influenzae_22121, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

Lm18364

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RiboSwitch type

FMN type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

123

Sequence

GTTCATCTTCGGGGCAGGGTGCAATTCCCGACCGGTGGTTAAAGTCCACGATCTGCTTTTTTAGCAGTTGACTCTGGTGTAATTCCAGGACCGACAGTATAGTCTGGATGGGAGAAGATGTT

Above is displayed the nucleotide sequence of the Listeria monocytogenes, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 26 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 37 nt. 4) Thiamine(T) in the sequence= 36 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 123 nt. 8) CG percentage of the sequence= 49.59% 9) *Melting temperature of the DNA based on the Wallace formula= 79.77oC 10) The entered DNA sequence(5-3) is-123 nt.: GTTCATCTTCGGGGCAGGGTGCAATTCCCGACCGGTGGTTAAAGTCCACGATCTGCTTTTTTAGCAGTTGACTCTGGTGTAATTCCAGGACCGACAGTATAGTCTGGATGGGAGAAGATGTTG 11) The complementary(Com) sequence(3-5) is-123 nt.: CAAGTAGAAGCCCCGTCCCACGTTAAGGGCTGGCCACCAATTTCAGGTGCTAGACGAAAAAATCGTCAACTGAGACCACATTAAGGTCCTGGCTGTCATATCAGACCTACCCTCTTCTACAAC 12) The reverse(Rev) sequence(3-5) is-123 nt.: GTTGTAGAAGAGGGTAGGTCTGATATGACAGCCAGGACCTTAATGTGGTCTCAGTTGACGATTTTTTCGTCTAGCACCTGAAATTGGTGGCCAGCCCTTAACGTGGGACGGGGCTTCTACTTG 13) The RevCom sequence(5-3) is-123 nt.: CAACATCTTCTCCCATCCAGACTATACTGTCGGTCCTGGAATTACACCAGAGTCAACTGCTAAAAAAGCAGATCGTGGACTTTAACCACCGGTCGGGAATTGCACCCTGCCCCGAAGATGAAC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-72 nt.: GTTCATCTTCGGGGCAGGGTGCAATTCCCGACCGGTGGTTAAAGTCCACGATCTGCTTTTTTAGCAGTTGAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-72 nt.: CAACATCTTCTCCCATCCAGACTATACTGTCGGTCCTGGAATTACACCAGAGTCAACTGCTAAAAAAGCAGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -37.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.15 kcal/mol. The frequency of the MFE structure in the ensemble is 15.47 %. The ensemble diversity is 10.83 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -37.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StAu14674

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RiboSwitch type

FMN type switch

Bacteria strain target

Staphylococcus aureus subsp_aureus_COL

Length of Switch in nucleotides

135

Sequence

ATTCATCTTCGGGGTCGGGTGTAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCTGCTAGTATGTATCATATTAGTGGCTGATCTAGTGAGATTCTAGAGCCGACAGTATAGTCTGGATGGGAGAAGATGGAG

Above is displayed the nucleotide sequence of the Staphylococcus aureus subsp_aureus_COL, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 39 nt. 4) Thiamine(T) in the sequence= 36 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 135 nt. 8) CG percentage of the sequence= 46.67% 9) *Melting temperature of the DNA based on the Wallace formula= 79.05oC 10) The entered DNA sequence(5-3) is-135 nt.: ATTCATCTTCGGGGTCGGGTGTAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCTGCTAGTAtgtaTCATATTAGTGGCTGATCTAGTGAGATTCTAGAGCCGACAGTATAGTCTGGATGGGAGAAGATGGAG 11) The complementary(Com) sequence(3-5) is-135 nt.: TAAGTAGAAGCCCCAGCCCACATTAAGGGTTGGCCGTCATTTATTTCGGACGCTGGACGATCATacatAGTATAATCACCGACTAGATCACTCTAAGATCTCGGCTGTCATATCAGACCTACCCTCTTCTACCTC 12) The reverse(Rev) sequence(3-5) is-135 nt.: GAGGTAGAAGAGGGTAGGTCTGATATGACAGCCGAGATCTTAGAGTGATCTAGTCGGTGATTATACTatgtATGATCGTCCAGCGTCCGAAATAAATGACGGCCAACCCTTAATGTGGGCTGGGGCTTCTACTTA 13) The RevCom sequence(5-3) is-135 nt.: CTCCATCTTCTCCCATCCAGACTATACTGTCGGCTCTAGAATCTCACTAGATCAGCCACTAATATGAtacaTACTAGCAGGTCGCAGGCTTTATTTACTGCCGGTTGGGAATTACACCCGACCCCGAAGATGAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-78 nt.: ATTCATCTTCGGGGTCGGGTGTAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCTGCTAGTAtgtaTCATATTAGT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-78 nt.: CTCCATCTTCTCCCATCCAGACTATACTGTCGGCTCTAGAATCTCACTAGATCAGCCACTAATATGAtacaTACTAGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus subsp_aureus_COL, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus subsp_aureus_COL, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -41.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -43.45 kcal/mol. The frequency of the MFE structure in the ensemble is 3.06 %. The ensemble diversity is 23.76 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -40.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus subsp_aureus_COL, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus subsp_aureus_COL, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StAuJH9

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RiboSwitch type

FMN type switch

Bacteria strain target

Staphylococcus aureus subsp_aureus_JH9

Length of Switch in nucleotides

136

Sequence

TAATTCTTTCGGGGCAGGGTGAAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCTGCTATATGTTTCATATTAGTGGCTGATCTAGTGAGATTCTAGAGCCGACAGTTAAAGTCTGGATGGGAGAAAGAATGT

Above is displayed the nucleotide sequence of the Staphylococcus aureus subsp_aureus_JH9, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 40 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 36 nt. 4) Thiamine(T) in the sequence= 37 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 136 nt. 8) CG percentage of the sequence= 43.38% 9) *Melting temperature of the DNA based on the Wallace formula= 77.74oC 10) The entered DNA sequence(5-3) is-136 nt.: TAATTCTTTCGGGGCAGGGTGAAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCTGCTAATAtgttTCATATTAGTGGCTGATCTAGTGAGATTCTAGAGCCGACAGtTAAAGTCTGGATGGGAGAAAGAATGT 11) The complementary(Com) sequence(3-5) is-136 nt.: ATTAAGAAAGCCCCGTCCCACTTTAAGGGTTGGCCGTCATTTATTTCGGACGCTGGACGATTATacaaAGTATAATCACCGACTAGATCACTCTAAGATCTCGGCTGTCaATTTCAGACCTACCCTCTTTCTTACA 12) The reverse(Rev) sequence(3-5) is-136 nt.: TGTAAGAAAGAGGGTAGGTCTGAAATtGACAGCCGAGATCTTAGAGTGATCTAGTCGGTGATTATACTttgtATAATCGTCCAGCGTCCGAAATAAATGACGGCCAACCCTTAAAGTGGGACGGGGCTTTCTTAAT 13) The RevCom sequence(5-3) is-136 nt.: ACATTCTTTCTCCCATCCAGACTTTAaCTGTCGGCTCTAGAATCTCACTAGATCAGCCACTAATATGAaacaTATTAGCAGGTCGCAGGCTTTATTTACTGCCGGTTGGGAATTTCACCCTGCCCCGAAAGAATTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-78 nt.: TAATTCTTTCGGGGCAGGGTGAAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCTGCTAATAtgttTCATATTAGT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-78 nt.: ACATTCTTTCTCCCATCCAGACTTTAaCTGTCGGCTCTAGAATCTCACTAGATCAGCCACTAATATGAaacaTATTAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus subsp_aureus_JH9, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus subsp_aureus_JH9, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -36.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.42 kcal/mol. The frequency of the MFE structure in the ensemble is 2.74 %. The ensemble diversity is 27.10 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -33.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus subsp_aureus_JH9, FMN type switch.

2D_Structure (A) (B)

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StEp1

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RiboSwitch type

FMN type switch

Bacteria strain target

Staphylococcus epidermidis_1

Length of Switch in nucleotides

139

Sequence

TATTTCTTTCGGGGCAGGGTGAAATTCCCAACCGGCAGTAAATTGAGCCTGCGACCCACTAATATTGTTTTTGATGTTAGTGGCTGATCTAGTGTGAATCTAGAGCCGACAGTTAGAGTCTGGATGGGAGAAAGAAGTT

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis_1, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 39 nt. 4) Thiamine(T) in the sequence= 41 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 139 nt. 8) CG percentage of the sequence= 44.60% 9) *Melting temperature of the DNA based on the Wallace formula= 78.35oC 10) The entered DNA sequence(5-3) is-139 nt.: TATTTCTTTCGGGGCAGGGTGAAATTCCCAACCGGCAGTAAATTGAGCCTGCGACCCACTAATAttgttttTGATGTTAGTGGCTGATCTAGTGTGAATCTAGAGCCGACAGtTAGAGTCTGGATGGGAGAAAGAAGTT 11) The complementary(Com) sequence(3-5) is-139 nt.: ATAAAGAAAGCCCCGTCCCACTTTAAGGGTTGGCCGTCATTTAACTCGGACGCTGGGTGATTATaacaaaaACTACAATCACCGACTAGATCACACTTAGATCTCGGCTGTCaATCTCAGACCTACCCTCTTTCTTCAA 12) The reverse(Rev) sequence(3-5) is-139 nt.: TTGAAGAAAGAGGGTAGGTCTGAGATtGACAGCCGAGATCTAAGTGTGATCTAGTCGGTGATTGTAGTttttgttATAATCACCCAGCGTCCGAGTTAAATGACGGCCAACCCTTAAAGTGGGACGGGGCTTTCTTTAT 13) The RevCom sequence(5-3) is-139 nt.: AACTTCTTTCTCCCATCCAGACTCTAaCTGTCGGCTCTAGATTCACACTAGATCAGCCACTAACATCAaaaacaaTATTAGTGGGTCGCAGGCTCAATTTACTGCCGGTTGGGAATTTCACCCTGCCCCGAAAGAAATA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-80 nt.: TATTTCTTTCGGGGCAGGGTGAAATTCCCAACCGGCAGTAAATTGAGCCTGCGACCCACTAATAttgttttTGATGTTAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-80 nt.: AACTTCTTTCTCCCATCCAGACTCTAaCTGTCGGCTCTAGATTCACACTAGATCAGCCACTAACATCAaaaacaaTATTA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis_1, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis_1, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -39.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -41.95 kcal/mol. The frequency of the MFE structure in the ensemble is 2.60 %. The ensemble diversity is 25.24 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis_1, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus epidermidis_1, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StEp100872

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RiboSwitch type

FMN type switch

Bacteria strain target

Staphylococcus epidermidis_2

Length of Switch in nucleotides

136

Sequence

ATTCATCTTCGGGGTAGGGTGTAATTCCCAACCGGCAGTAATCTAAGCCTGCGACGACAACGTATTAATTTTTGCTTTGTCTTGATTCAGTGAGAGTCTGAAGCCGACAGTATAGTCTGGATGGGAGAAGATGGAG

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis_2, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 35 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 38 nt. 4) Thiamine(T) in the sequence= 39 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 136 nt. 8) CG percentage of the sequence= 45.59% 9) *Melting temperature of the DNA based on the Wallace formula= 78.65oC 10) The entered DNA sequence(5-3) is-136 nt.: ATTCATCTTCGGGGTAGGGTGTAATTCCCAACCGGCAGTAATCTAAGCCTGCGACGACAACGTattaatTTTTGCTTTGTCTTGATTCAGTGAGAGTCTGAAGCCGACAGTATAGTCTGGATGGGAGAAGATGGAG 11) The complementary(Com) sequence(3-5) is-136 nt.: TAAGTAGAAGCCCCATCCCACATTAAGGGTTGGCCGTCATTAGATTCGGACGCTGCTGTTGCAtaattaAAAACGAAACAGAACTAAGTCACTCTCAGACTTCGGCTGTCATATCAGACCTACCCTCTTCTACCTC 12) The reverse(Rev) sequence(3-5) is-136 nt.: GAGGTAGAAGAGGGTAGGTCTGATATGACAGCCGAAGTCTGAGAGTGACTTAGTTCTGTTTCGTTTTtaattaTGCAACAGCAGCGTCCGAATCTAATGACGGCCAACCCTTAATGTGGGATGGGGCTTCTACTTA 13) The RevCom sequence(5-3) is-136 nt.: CTCCATCTTCTCCCATCCAGACTATACTGTCGGCTTCAGACTCTCACTGAATCAAGACAAAGCAAAAattaatACGTTGTCGTCGCAGGCTTAGATTACTGCCGGTTGGGAATTACACCCTACCCCGAAGATGAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-78 nt.: ATTCATCTTCGGGGTAGGGTGTAATTCCCAACCGGCAGTAATCTAAGCCTGCGACGACAACGTattaatTTTTGCTTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-78 nt.: CTCCATCTTCTCCCATCCAGACTATACTGTCGGCTTCAGACTCTCACTGAATCAAGACAAAGCAAAAattaatACGTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis_2, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis_2, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -38.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -40.63 kcal/mol. The frequency of the MFE structure in the ensemble is 5.13 %. The ensemble diversity is 16.92 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -37.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis_2, FMN type switch.

2D_Structure (A) (B)

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

ATCC_15305

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RiboSwitch type

FMN type switch

Bacteria strain target

Staphylococcus saprophyticus subsp saprophyticus ATCC_15305

Length of Switch in nucleotides

136

Sequence

ATTCATCTTCGGGGTAGGGTGCAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCCATTTTATTATATATAATAAAATGGCTGATCTAGTGAAAATCTAGAGCCGACAGTAAAGTCTGGATGGGAGAAGATGGAG

Above is displayed the nucleotide sequence of the Staphylococcus saprophyticus subsp saprophyticus ATCC_15305, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 45 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 34 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 136 nt. 8) CG percentage of the sequence= 41.91% 9) *Melting temperature of the DNA based on the Wallace formula= 77.14oC 10) The entered DNA sequence(5-3) is-136 nt.: ATTCATCTTCGGGGTAGGGTGCAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCCATTTTATtatatATAATAAAATGGCTGATCTAGTGAAAATCTAGAGCCGACAGTAAAGTCTGGATGGGAGAAGATGGAG 11) The complementary(Com) sequence(3-5) is-136 nt.: TAAGTAGAAGCCCCATCCCACGTTAAGGGTTGGCCGTCATTTATTTCGGACGCTGGGTAAAATAatataTATTATTTTACCGACTAGATCACTTTTAGATCTCGGCTGTCATTTCAGACCTACCCTCTTCTACCTC 12) The reverse(Rev) sequence(3-5) is-136 nt.: GAGGTAGAAGAGGGTAGGTCTGAAATGACAGCCGAGATCTAAAAGTGATCTAGTCGGTAAAATAATAtatatTATTTTACCCAGCGTCCGAAATAAATGACGGCCAACCCTTAACGTGGGATGGGGCTTCTACTTA 13) The RevCom sequence(5-3) is-136 nt.: CTCCATCTTCTCCCATCCAGACTTTACTGTCGGCTCTAGATTTTCACTAGATCAGCCATTTTATTATatataATAAAATGGGTCGCAGGCTTTATTTACTGCCGGTTGGGAATTGCACCCTACCCCGAAGATGAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-78 nt.: ATTCATCTTCGGGGTAGGGTGCAATTCCCAACCGGCAGTAAATAAAGCCTGCGACCCATTTTATtatatATAATAAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-78 nt.: CTCCATCTTCTCCCATCCAGACTTTACTGTCGGCTCTAGATTTTCACTAGATCAGCCATTTTATTATatataATAAAA ?

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus saprophyticus subsp saprophyticus ATCC_15305, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus saprophyticus subsp saprophyticus ATCC_15305, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -40.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -42.25 kcal/mol. The frequency of the MFE structure in the ensemble is 9.59 %. The ensemble diversity is 15.46 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -39.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus saprophyticus subsp saprophyticus ATCC_15305, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus saprophyticus subsp saprophyticus ATCC_15305, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StA909

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RiboSwitch type

FMN type switch

Bacteria strain target

Streptococcus agalactiae A909

Length of Switch in nucleotides

115

Sequence

GAATTTCTTCGGGGTCAGGTGAAAATCCTAACCGGCGGTATAGTCCGCGAGCTTTCGAGCATGAACTGGTGTGATTCCAGTACCGACAGTAAAGTCTGGATGAGAGAAGAATTCA

Above is displayed the nucleotide sequence of the Streptococcus agalactiae A909, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 33 nt. 4) Thiamine(T) in the sequence= 28 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 115 nt. 8) CG percentage of the sequence= 47.83% 9) *Melting temperature of the DNA based on the Wallace formula= 78.66oC 10) The entered DNA sequence(5-3) is-115 nt.: GAATTTCTTCGGGGTCAGGTGAAAATCCTAACCGGCGGTATAGTCCGCGAGCTTTCGAGCATGAACTGGTGTGATTCCAGTACCGACAGTAAAGTCTGGATGAGAGAAGAATTCA 11) The complementary(Com) sequence(3-5) is-115 nt.: CTTAAAGAAGCCCCAGTCCACTTTTAGGATTGGCCGCCATATCAGGCGCTCGAAAGCTCGTACTTGACCACACTAAGGTCATGGCTGTCATTTCAGACCTACTCTCTTCTTAAGT 12) The reverse(Rev) sequence(3-5) is-115 nt.: ACTTAAGAAGAGAGTAGGTCTGAAATGACAGCCATGACCTTAGTGTGGTCAAGTACGAGCTTTCGAGCGCCTGATATGGCGGCCAATCCTAAAAGTGGACTGGGGCTTCTTTAAG 13) The RevCom sequence(5-3) is-115 nt.: TGAATTCTTCTCTCATCCAGACTTTACTGTCGGTACTGGAATCACACCAGTTCATGCTCGAAAGCTCGCGGACTATACCGCCGGTTAGGATTTTCACCTGACCCCGAAGAAATTC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-68 nt.: GAATTTCTTCGGGGTCAGGTGAAAATCCTAACCGGCGGTATAGTCCGCGAGCTTTCGAGCATGAACTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-68 nt.: TGAATTCTTCTCTCATCCAGACTTTACTGTCGGTACTGGAATCACACCAGTTCATGCTCGAAAGCTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus agalactiae A909, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus agalactiae A909, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -32.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -34.04 kcal/mol. The frequency of the MFE structure in the ensemble is 11.33 %. The ensemble diversity is 9.31 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -32.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus agalactiae A909, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus agalactiae A909, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StMGAS10750

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RiboSwitch type

FMN type switch

Bacteria strain target

Streptococcus pyogenes MGAS10750

Length of Switch in nucleotides

124

Sequence

AAGTGTCTTCAGGGCAGGGTGTGATTCCCGACCGGCGGTGACTAGTAACTAGAAGTCCGCGAGCGCAAGCTGATGTGGTGTAACTCCACAACCGACAGTATAGTCTGGATGAGAGAAGACCGGG

Above is displayed the nucleotide sequence of the Streptococcus pyogenes MGAS10750, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 41 nt. 4) Thiamine(T) in the sequence= 24 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 124 nt. 8) CG percentage of the sequence= 54.84% 9) *Melting temperature of the DNA based on the Wallace formula= 81.96oC 10) The entered DNA sequence(5-3) is-124 nt.: AAGTGTCTTCAGGGCAGGGTGTGATTCCCGACCGGCGGTGACTAGTAACTAGAAGTCCGCGAGCGCAAGCTGATGTGGTGTAACTCCACAACCGACAGTATAGTCTGGATGAGAGAAGACCGGG 11) The complementary(Com) sequence(3-5) is-124 nt.: TTCACAGAAGTCCCGTCCCACACTAAGGGCTGGCCGCCACTGATCATTGATCTTCAGGCGCTCGCGTTCGACTACACCACATTGAGGTGTTGGCTGTCATATCAGACCTACTCTCTTCTGGCCC 12) The reverse(Rev) sequence(3-5) is-124 nt.: GGGCCAGAAGAGAGTAGGTCTGATATGACAGCCAACACCTCAATGTGGTGTAGTCGAACGCGAGCGCCTGAAGATCAATGATCAGTGGCGGCCAGCCCTTAGTGTGGGACGGGACTTCTGTGAA 13) The RevCom sequence(5-3) is-124 nt.: CCCGGTCTTCTCTCATCCAGACTATACTGTCGGTTGTGGAGTTACACCACATCAGCTTGCGCTCGCGGACTTCTAGTTACTAGTCACCGCCGGTCGGGAATCACACCCTGCCCTGAAGACACTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-72 nt.: AAGTGTCTTCAGGGCAGGGTGTGATTCCCGACCGGCGGTGACTAGTAACTAGAAGTCCGCGAGCGCAAGCTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-72 nt.: CCCGGTCTTCTCTCATCCAGACTATACTGTCGGTTGTGGAGTTACACCACATCAGCTTGCGCTCGCGGACTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus pyogenes MGAS10750, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus pyogenes MGAS10750, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -36.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -37.75 kcal/mol. The frequency of the MFE structure in the ensemble is 21.51 %. The ensemble diversity is 4.79 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus pyogenes MGAS10750, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus pyogenes MGAS10750, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StMGAS2092

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RiboSwitch type

FMN type switch

Bacteria strain target

Streptococcus pyogenes MGAS2092

Length of Switch in nucleotides

125

Sequence

AAGTGTCTTCAGGGCAGGGTGTGATTCCCGACCGGCGGTGACTAAGTAACTAGAAGTCCGCGAGCGCAAGCTGATGTGGTGTAACTCCACAACCGACAGTATAGTCTGGATGAGAGAAGACCGGG

Above is displayed the nucleotide sequence of the Streptococcus pyogenes MGAS2092, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 41 nt. 4) Thiamine(T) in the sequence= 24 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 125 nt. 8) CG percentage of the sequence= 54.40% 9) *Melting temperature of the DNA based on the Wallace formula= 81.82oC 10) The entered DNA sequence(5-3) is-125 nt.: AAGTGTCTTCAGGGCAGGGTGTGATTCCCGACCGGCGGTGACTAAGTAACTAGAAGTCCGCGAGCGCAAGCTGATGTGGTGTAACTCCACAACCGACAGTATAGTCTGGATGAGAGAAGACCGGG 11) The complementary(Com) sequence(3-5) is-125 nt.: TTCACAGAAGTCCCGTCCCACACTAAGGGCTGGCCGCCACTGATTCATTGATCTTCAGGCGCTCGCGTTCGACTACACCACATTGAGGTGTTGGCTGTCATATCAGACCTACTCTCTTCTGGCCC 12) The reverse(Rev) sequence(3-5) is-125 nt.: GGGCCAGAAGAGAGTAGGTCTGATATGACAGCCAACACCTCAATGTGGTGTAGTCGAACGCGAGCGCCTGAAGATCAATGAATCAGTGGCGGCCAGCCCTTAGTGTGGGACGGGACTTCTGTGAA 13) The RevCom sequence(5-3) is-125 nt.: CCCGGTCTTCTCTCATCCAGACTATACTGTCGGTTGTGGAGTTACACCACATCAGCTTGCGCTCGCGGACTTCTAGTTACTTAGTCACCGCCGGTCGGGAATCACACCCTGCCCTGAAGACACTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-73 nt.: AAGTGTCTTCAGGGCAGGGTGTGATTCCCGACCGGCGGTGACTAAGTAACTAGAAGTCCGCGAGCGCAAGCTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-73 nt.: CCCGGTCTTCTCTCATCCAGACTATACTGTCGGTTGTGGAGTTACACCACATCAGCTTGCGCTCGCGGACTTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus pyogenes MGAS2092, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus pyogenes MGAS2092, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -35.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -36.26 kcal/mol. The frequency of the MFE structure in the ensemble is 17.90 %. The ensemble diversity is 6.11 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -35.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus pyogenes MGAS2092, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus pyogenes MGAS2092, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

StJJA1763

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RiboSwitch type

FMN type switch

Bacteria strain target

Streptococcus pneumoniae JJA

Length of Switch in nucleotides

115

Sequence

AACTATCTTCAGGGCAGGGTGCAATTCCCTACCGGTGGTATAGCCCACGAGCCGAAAGGCATGATTTGGTGAAATTCCAAAGCCGACAGTATAGTCTGGATGAAAGAAGATAAAA

Above is displayed the nucleotide sequence of the Streptococcus pneumoniae JJA, FMN type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 38 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 30 nt. 4) Thiamine(T) in the sequence= 24 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 115 nt. 8) CG percentage of the sequence= 46.09% 9) *Melting temperature of the DNA based on the Wallace formula= 77.95oC 10) The entered DNA sequence(5-3) is-115 nt.: AACTATCTTCAGGGCAGGGTGCAATTCCCTACCGGTGGTATAGCCCACGAGCCGAAAGGCATGATTTGGTGAAATTCCAAAGCCGACAGTATAGTCTGGATGAAAGAAGATAAAA 11) The complementary(Com) sequence(3-5) is-115 nt.: TTGATAGAAGTCCCGTCCCACGTTAAGGGATGGCCACCATATCGGGTGCTCGGCTTTCCGTACTAAACCACTTTAAGGTTTCGGCTGTCATATCAGACCTACTTTCTTCTATTTT 12) The reverse(Rev) sequence(3-5) is-115 nt.: AAAATAGAAGAAAGTAGGTCTGATATGACAGCCGAAACCTTAAAGTGGTTTAGTACGGAAAGCCGAGCACCCGATATGGTGGCCATCCCTTAACGTGGGACGGGACTTCTATCAA 13) The RevCom sequence(5-3) is-115 nt.: TTTTATCTTCTTTCATCCAGACTATACTGTCGGCTTTGGAATTTCACCAAATCATGCCTTTCGGCTCGTGGGCTATACCACCGGTAGGGAATTGCACCCTGCCCTGAAGATAGTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-68 nt.: AACTATCTTCAGGGCAGGGTGCAATTCCCTACCGGTGGTATAGCCCACGAGCCGAAAGGCATGATTTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-68 nt.: TTTTATCTTCTTTCATCCAGACTATACTGTCGGCTTTGGAATTTCACCAAATCATGCCTTTCGGCTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus pneumoniae JJA, FMN type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus pneumoniae JJA, FMN type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -33.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -33.79 kcal/mol. The frequency of the MFE structure in the ensemble is 27.56 %. The ensemble diversity is 9.26 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -33.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus pneumoniae JJA, FMN type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus pneumoniae JJA, FMN type switch.

Multiple alignment of the FMN type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

RiboSwitch_ID:

BaSub10231

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RiboSwitch type

GlmS type switch

Bacteria strain target

Bacillus subtilis 1

Length of Switch in nucleotides

168

Sequence

CCTATAATTATAGCGCCCGAACTAAGCGCCCGGAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTCGCGGATCCTCCCGGCTGAGTGTGCAGATCACAGCCGTAAGAATTTCTTCAAACCAAGGGGGTGACTCCTTGAACAAAGAGAAATCAC

Above is displayed the nucleotide sequence of the Bacillus subtilis 1, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 50 nt. 2) Cytosine(C) in the sequence= 38 nt. 3) Guanine(G) in the sequence= 42 nt. 4) Thiamine(T) in the sequence= 38 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 168 nt. 8) CG percentage of the sequence= 47.62% 9) *Melting temperature of the DNA based on the Wallace formula= 80.42oC 10) The entered DNA sequence(5-3) is-168 nt.: CCTATAATTATAGCGCCCGAACTAAGCGCCCGGAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTCGCGGATCCTCCCGGCTGAGTGTGCAGATCACAGCCGTAAGAATTTCTTCAAACCAAGGGGGTGACTCCTTGAACAAAGAGAAATCACATGATCTT 11) The complementary(Com) sequence(3-5) is-168 nt.: GGATATTAATATCGCGGGCTTGATTCGCGGGCCTTTTTCCGAATCAACTGCTCCTACCTCCAATAGCTTAAAGCGCCTAGGAGGGCCGACTCACACGTCTAGTGTCGGCATTCTTAAAGAAGTTTGGTTCCCCCACTGAGGAACTTGTTTCTCTTTAGTGTACTAGAA 12) The reverse(Rev) sequence(3-5) is-168 nt.: TTCTAGTACACTAAAGAGAAACAAGTTCCTCAGTGGGGGAACCAAACTTCTTTAAGAATGCCGACACTAGACGTGTGAGTCGGCCCTCCTAGGCGCTTTAAGCTATTGGAGGTAGGAGCAGTTGATTCGGAAAAAGGCCCGCGAATCAAGCCCGCGATATTAATATCC 13) The RevCom sequence(5-3) is-168 nt.: AAGATCATGTGATTTCTCTTTGTTCAAGGAGTCACCCCCTTGGTTTGAAGAAATTCTTACGGCTGTGATCTGCACACTCAGCCGGGAGGATCCGCGAAATTCGATAACCTCCATCCTCGTCAACTAAGCCTTTTTCCGGGCGCTTAGTTCGGGCGCTATAATTATAGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-94 nt.: CCTATAATTATAGCGCCCGAACTAAGCGCCCGGAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTCGCGGATCCTCCCGGCTGAGTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-94 nt.: AAGATCATGTGATTTCTCTTTGTTCAAGGAGTCACCCCCTTGGTTTGAAGAAATTCTTACGGCTGTGATCTGCACACTCAGCCGGGAGGATCCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis 1, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis 1, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -43.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble prediction. The free energy of the thermodynamic ensemble is -47.11 kcal/mol. The frequency of the MFE structure in the ensemble is 0.15 %. The ensemble diversity is 24.75 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -40.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis 1, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis 1, GlmS type switch.

Multiple alignment of the GlmS type switches

Below is presented the sequences alignment of all the GlmS type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the GlmS type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the GlmS riboswitches and shorter motifs based on the general one: 1) N{0,9}AN?AGCGCCN?GRRCTN?ARN{0,15}YTN?AGTTGACGAGGARRRGRN?TN?ATCGARN{0,3}TCGGCGGRTGYCYYYCGGN{0,9}CN{0,2}YCGYYARN{0,2}YN{0,6}YAAAN{0,6}RRGTGAYYN{0,6}ACARAGN{0,5}RN{0,2}RN{0,7}RN? 2) AGTTGACGAGGARRRGR 3) TCGGCGGRTGYCYYYCGG Motifs identified amongst the GlmS riboswitches based on the sequences alignment: 1) GMCGARRW 2) MYCSAW Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

The table displays known human pathogenic bacteria bearing the GlmS type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BaSub66331

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RiboSwitch type

GlmS type switch

Bacteria strain target

Bacillus subtilis subsp spizizenii ATCC_6633_1

Length of Switch in nucleotides

171

Sequence

CCTATAATTATAGCGCCCGAACTAAGCGCCCGAAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTTCGGCGGATGCCTCCCGGCTGATTATGCAGATCACAGCCGTAAGGATTTCTTCAAACCAAGGGGGTAACTCCTTGAACAAAGAGAAATCACATGATCTT

Above is displayed the nucleotide sequence of the Bacillus subtilis subsp spizizenii ATCC_6633_1, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 52 nt. 2) Cytosine(C) in the sequence= 38 nt. 3) Guanine(G) in the sequence= 41 nt. 4) Thiamine(T) in the sequence= 40 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 171 nt. 8) CG percentage of the sequence= 46.20% 9) *Melting temperature of the DNA based on the Wallace formula= 79.91oC 10) The entered DNA sequence(5-3) is-171 nt.: CCTATAATTATAGCGCCCGAACTAAGCGCCCGAAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTTCGGCGGATGCCTCCCGGCTGATTATGCAGATCACAGCCGTAAGGATTTCTTCAAACCAAGGGGGTAACTCCTTGAACAAAGAGAAATCACATGATCTT 11) The complementary(Com) sequence(3-5) is-171 nt.: GGATATTAATATCGCGGGCTTGATTCGCGGGCTTTTTTCCGAATCAACTGCTCCTACCTCCAATAGCTTAAAAGCCGCCTACGGAGGGCCGACTAATACGTCTAGTGTCGGCATTCCTAAAGAAGTTTGGTTCCCCCATTGAGGAACTTGTTTCTCTTTAGTGTACTAGAA 12) The reverse(Rev) sequence(3-5) is-171 nt.: TTCTAGTACACTAAAGAGAAACAAGTTCCTCAATGGGGGAACCAAACTTCTTTAGGAATGCCGACACTAGACGTATTAGTCGGCCCTCCGTAGGCGGCTTTTAAGCTATTGGAGGTAGGAGCAGTTGATTCGGAAAAAAGCCCGCGAATCAAGCCCGCGATATTAATATCC 13) The RevCom sequence(5-3) is-171 nt.: AAGATCATGTGATTTCTCTTTGTTCAAGGAGTTACCCCCTTGGTTTGAAGAAATCCTTACGGCTGTGATCTGCATAATCAGCCGGGAGGCATCCGCCGAAAATTCGATAACCTCCATCCTCGTCAACTAAGCCTTTTTTCGGGCGCTTAGTTCGGGCGCTATAATTATAGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-96 nt.: CCTATAATTATAGCGCCCGAACTAAGCGCCCGAAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTTCGGCGGATGCCTCCCGGCTGATT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-96 nt.: AAGATCATGTGATTTCTCTTTGTTCAAGGAGTTACCCCCTTGGTTTGAAGAAATCCTTACGGCTGTGATCTGCATAATCAGCCGGGAGGCATCCGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis subsp spizizenii ATCC_6633_1, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis subsp spizizenii ATCC_6633_1, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -49.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble prediction. The free energy of the thermodynamic ensemble is -52.12 kcal/mol. The frequency of the MFE structure in the ensemble is 0.64 %. The ensemble diversity is 17.72. The centroid secondary structure in dot-bracket notation with a minimum free energy of -40.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis subsp spizizenii ATCC_6633_1, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis subsp spizizenii ATCC_6633_1, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

Motifs identified amongst the GlmS riboswitches based on the sequences alignment: 1) GMCGARRW 2) MYCSAW 3) YCRRC 4) HMARA

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

EnFaV5831

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RiboSwitch type

GlmS type switch

Bacteria strain target

Enterococcus faecalis_V583

Length of Switch in nucleotides

148

Sequence

CAATATCGGATAGCGCCAGACCTGAACGTTCAGGTGACGAGGAGAGAGCTTATCGAAGATTCGGCGGGTGGCTCTAGGGACTGCACTCTACAGATAACAAAGAAAAACTAATTGTGAAGTTAGAACAAAGCGGTTATCACGCAGGTAG

Above is displayed the nucleotide sequence of the Enterococcus faecalis_V583, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 49 nt. 2) Cytosine(C) in the sequence= 28 nt. 3) Guanine(G) in the sequence= 42 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 148 nt. 8) CG percentage of the sequence= 47.30% 9) *Melting temperature of the DNA based on the Wallace formula= 79.75oC 10) The entered DNA sequence(5-3) is-148 nt.: CAATATCGGATAGCGCCAGACCTGAACGTTCAGGTGACGAGGAGAGAGCTTATCGAAGATTCGGCGGGTGGCTCTAGGGACTGCACTCTACAGATAACAAAGAAAAACTAATTGTGAAGTTAGAACAAAGCGGTTATCACGCAGGTAG 11) The complementary(Com) sequence(3-5) is-148 nt.: GTTATAGCCTATCGCGGTCTGGACTTGCAAGTCCACTGCTCCTCTCTCGAATAGCTTCTAAGCCGCCCACCGAGATCCCTGACGTGAGATGTCTATTGTTTCTTTTTGATTAACACTTCAATCTTGTTTCGCCAATAGTGCGTCCATC 12) The reverse(Rev) sequence(3-5) is-148 nt.: GATGGACGCACTATTGGCGAAACAAGATTGAAGTGTTAATCAAAAAGAAACAATAGACATCTCACGTCAGGGATCTCGGTGGGCGGCTTAGAAGCTATTCGAGAGAGGAGCAGTGGACTTGCAAGTCCAGACCGCGATAGGCTATAAC 13) The RevCom sequence(5-3) is-148 nt.: CTACCTGCGTGATAACCGCTTTGTTCTAACTTCACAATTAGTTTTTCTTTGTTATCTGTAGAGTGCAGTCCCTAGAGCCACCCGCCGAATCTTCGATAAGCTCTCTCCTCGTCACCTGAACGTTCAGGTCTGGCGCTATCCGATATTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-84 nt.: CAATATCGGATAGCGCCAGACCTGAACGTTCAGGTGACGAGGAGAGAGCTTATCGAAGATTCGGCGGGTGGCTCTAGGGACTGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-84 nt.:

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecalis_V583, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecalis_V583, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -32.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -34.44 kcal/mol. The frequency of the MFE structure in the ensemble is 3.10 %. The ensemble diversity is 27.09. The centroid secondary structure in dot-bracket notation with a minimum free energy of -23.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecalis_V583, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecalis_V583, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

LmF236501

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RiboSwitch type

GlmS type switch

Bacteria strain target

Listeria moncytogenes str 4b F2365_1

Length of Switch in nucleotides

196

Sequence

AATTAAATAGAAGCGCCAGAACTGATTGGGACGAAAATACTTGAAGGTGAAATCCCTGAAAAGTAAACAGTCAGTTGACGAGGAGGAGATTAATCGAAGTTTCGGCGGGAGTCTCCCGGCTGTGCATGCAGTCGTTAAGTCTTACTTACAAATCACTTGGGTGACCAAGTGGACAGAGTAGTAATGAAACATGTTT

Above is displayed the nucleotide sequence of the Listeria moncytogenes str 4b F2365_1, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 65 nt. 2) Cytosine(C) in the sequence= 32 nt. 3) Guanine(G) in the sequence= 52 nt. 4) Thiamine(T) in the sequence= 47 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 196 nt. 8) CG percentage of the sequence= 42.86% 9) *Melting temperature of the DNA based on the Wallace formula= 79.04oC 10) The entered DNA sequence(5-3) is-196 nt.: AATTAAATAGAAGCGCCAGAACTGATTGGGACGAAAATACTTGAAGGTGAAATCCCTGAAAAGTAAACAGTCAGTTGACGAGGAGGAGATTAATCGAAGTTTCGGCGGGAGTCTCCCGGCTGTGCATGCAGTCGTTAAGTCTTACTTACAAATCACTTGGGTGACCAAGTGGACAGAGTAGTAATGAAACATGTTT 11) The complementary(Com) sequence(3-5) is-196 nt.: TTAATTTATCTTCGCGGTCTTGACTAACCCTGCTTTTATGAACTTCCACTTTAGGGACTTTTCATTTGTCAGTCAACTGCTCCTCCTCTAATTAGCTTCAAAGCCGCCCTCAGAGGGCCGACACGTACGTCAGCAATTCAGAATGAATGTTTAGTGAACCCACTGGTTCACCTGTCTCATCATTACTTTGTACAAA 12) The reverse(Rev) sequence(3-5) is-196 nt.: TTTGTACAAAGTAATGATGAGACAGGTGAACCAGTGGGTTCACTAAACATTCATTCTGAATTGCTGACGTACGTGTCGGCCCTCTGAGGGCGGCTTTGAAGCTAATTAGAGGAGGAGCAGTTGACTGACAAATGAAAAGTCCCTAAAGTGGAAGTTCATAAAAGCAGGGTTAGTCAAGACCGCGAAGATAAATTAA 13) The RevCom sequence(5-3) is-196 nt.: AAACATGTTTCATTACTACTCTGTCCACTTGGTCACCCAAGTGATTTGTAAGTAAGACTTAACGACTGCATGCACAGCCGGGAGACTCCCGCCGAAACTTCGATTAATCTCCTCCTCGTCAACTGACTGTTTACTTTTCAGGGATTTCACCTTCAAGTATTTTCGTCCCAATCAGTTCTGGCGCTTCTATTTAATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-108 nt.: AATTAAATAGAAGCGCCAGAACTGATTGGGACGAAAATACTTGAAGGTGAAATCCCTGAAAAGTAAACAGTCAGTTGACGAGGAGGAGATTAATCGAAGTTTCGGCGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-108 nt.: AAACATGTTTCATTACTACTCTGTCCACTTGGTCACCCAAGTGATTTGTAAGTAAGACTTAACGACTGCATGCACAGCCGGGAGACTCCCGCCGAAACTTCGATTAAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria moncytogenes str 4b F2365_1, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria moncytogenes str 4b F2365_1, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -40.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -52.43 kcal/mol. The frequency of the MFE structure in the ensemble is 0.38 %. The ensemble diversity is 26.45. The centroid secondary structure in dot-bracket notation with a minimum free energy of -44.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria moncytogenes str 4b F2365_1, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria moncytogenes str 4b F2365_1, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

LMFSL16502

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RiboSwitch type

GlmS type switch

Bacteria strain target

Listeria monocytogenes FSL_N3_165

Length of Switch in nucleotides

195

Sequence

AATTGAATAGAAGCGCCAGAACTGATTGGGACGAAAATGCTTGAAGGTGAAATCCCTGAAAAGTATCGATCAGTTGACGAGGAGGAGATTAATCGAAGTTTCGGCGGGAGTCTCCCGGCTGTGCATGCAGTCGTTAAGTCTTACTTACAAATCATTTGGGTGACCAAGTGGACAGAGTAGTAATGAAACATGCTT

Above is displayed the nucleotide sequence of the Listeria monocytogenes FSL_N3_165, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 61 nt. 2) Cytosine(C) in the sequence= 32 nt. 3) Guanine(G) in the sequence= 54 nt. 4) Thiamine(T) in the sequence= 48 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 195 nt 8) CG percentage of the sequence= 44.10% 9) *Melting temperature of the DNA based on the Wallace formula= 79.53oC 10) The entered DNA sequence(5-3) is-195 nt.: AATTGAATAGAAGCGCCAGAACTGATTGGGACGAAAATGCTTGAAGGTGAAATCCCTGAAAAGTATCGATCAGTTGACGAGGAGGAGATTAATCGAAGTTTCGGCGGGAGTCTCCCGGCTGTGCATGCAGTCGTTAAGTCTTACTTACAAATCATTTGGGTGACCAAGTGGACAGAGTAGTAATGAAACATGCTT 11) The complementary(Com) sequence(3-5) is-195 nt.: TTAACTTATCTTCGCGGTCTTGACTAACCCTGCTTTTACGAACTTCCACTTTAGGGACTTTTCATAGCTAGTCAACTGCTCCTCCTCTAATTAGCTTCAAAGCCGCCCTCAGAGGGCCGACACGTACGTCAGCAATTCAGAATGAATGTTTAGTAAACCCACTGGTTCACCTGTCTCATCATTACTTTGTACGAA 12) The reverse(Rev) sequence(3-5) is-195 nt.: TTCGTACAAAGTAATGATGAGACAGGTGAACCAGTGGGTTTACTAAACATTCATTCTGAATTGCTGACGTACGTGTCGGCCCTCTGAGGGCGGCTTTGAAGCTAATTAGAGGAGGAGCAGTTGACTAGCTATGAAAAGTCCCTAAAGTGGAAGTTCGTAAAAGCAGGGTTAGTCAAGACCGCGAAGATAAGTTAA 13) The RevCom sequence(5-3) is-195 nt.: AAGCATGTTTCATTACTACTCTGTCCACTTGGTCACCCAAATGATTTGTAAGTAAGACTTAACGACTGCATGCACAGCCGGGAGACTCCCGCCGAAACTTCGATTAATCTCCTCCTCGTCAACTGATCGATACTTTTCAGGGATTTCACCTTCAAGCATTTTCGTCCCAATCAGTTCTGGCGCTTCTATTCAATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-108 nt.: AATTGAATAGAAGCGCCAGAACTGATTGGGACGAAAATGCTTGAAGGTGAAATCCCTGAAAAGTATCGATCAGTTGACGAGGAGGAGATTAATCGAAGTTTCGGCGGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-108 nt.: AAGCATGTTTCATTACTACTCTGTCCACTTGGTCACCCAAATGATTTGTAAGTAAGACTTAACGACTGCATGCACAGCCGGGAGACTCCCGCCGAAACTTCGATTAAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes FSL_N3_165, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes FSL_N3_165, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -49.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -52.43 kcal/mol. The frequency of the MFE structure in the ensemble is 0.38 %. The ensemble diversity is 26.45. The centroid secondary structure in dot-bracket notation with a minimum free energy of -44.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes FSL_N3_165, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes FSL_N3_165, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

SA1094261

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RiboSwitch type

GlmS type switch

Bacteria strain target

Staphylococcus aureus

Length of Switch in nucleotides

217

Sequence

AGTACAGTTAAAGCGCCTGTGCAAATAAATATTTGTATTTGAAGATTAAAGGTTAATATATGAGTGGCCTTTATAGAGTGCAATATATGTATTTGTAGACGAGGAGGATAGTGATCGAATAGATCGGCGGATGCTATCCCGGATGTGGCTCATTCGTTAGCTTATTAAGTAAAACATTAGGGTGACTTAATGGACAAAGTTAATAAGATCGCCAGAA

Above is displayed the nucleotide sequence of the Staphylococcus aureus, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 73 nt. 2) Cytosine(C) in the sequence= 26 nt. 3) Guanine(G) in the sequence= 53 nt. 4) Thiamine(T) in the sequence= 65 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 217 nt. 8) CG percentage of the sequence= 36.41% 9) *Melting temperature of the DNA based on the Wallace formula= 76.73oC 10) The entered DNA sequence(5-3) is-217 nt.: AGTACAGTTAAAGCGCCTGTGCAAATAAATATTTGTATTTGAAGATTAAAGGTTAATATATGAGTGGCCTTTATAGAGTGCAATATATGTATTTGTAGACGAGGAGGATAGTGATCGAATAGATCGGCGGATGCTATCCCGGATGTGGCTCATTCGTTAGCTTATTAAGTAAAACATTAGGGTGACTTAATGGACAAAGTTAATAAGATCGCCAGAA 11) The complementary(Com) sequence(3-5) is-217 nt.: TCATGTCAATTTCGCGGACACGTTTATTTATAAACATAAACTTCTAATTTCCAATTATATACTCACCGGAAATATCTCACGTTATATACATAAACATCTGCTCCTCCTATCACTAGCTTATCTAGCCGCCTACGATAGGGCCTACACCGAGTAAGCAATCGAATAATTCATTTTGTAATCCCACTGAATTACCTGTTTCAATTATTCTAGCGGTCTT 12) The reverse(Rev) sequence(3-5) is-217 nt.: AAGACCGCTAGAATAATTGAAACAGGTAATTCAGTGGGATTACAAAATGAATTATTCGATTGCTTACTCGGTGTAGGCCCTATCGTAGGCGGCTAGATAAGCTAGTGATAGGAGGAGCAGATGTTTATGTATATAACGTGAGATATTTCCGGTGAGTATATAATTGGAAATTAGAAGTTTATGTTTATAAATAAACGTGTCCGCGAAATTGACATGA 13) The RevCom sequence(5-3) is-217 nt.: TTCTGGCGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGCACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-119 nt.: AGTACAGTTAAAGCGCCTGTGCAAATAAATATTTGTATTTGAAGATTAAAGGTTAATATATGAGTGGCCTTTATAGAGTGCAATATATGTATTTGTAGACGAGGAGGATAGTGATCGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-119 nt.: TTCTGGCGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -56.20 kcal/mol. The frequency of the MFE structure in the ensemble is 3.51 %. The ensemble diversity is 17.00. The centroid secondary structure in dot-bracket notation with a minimum free energy of -54.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

SE231101

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RiboSwitch type

GlmS type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

218

Sequence

TTAATAATTAAAGCGCCTGTGCAAAATACCTAAATAGTTATCAAGTATTAAAAGTTAAAATAGTAGAACTTTTATAGATAACGATTTGGATTTTGTAGACGAGGAGGATAGTGATCGAATCAGATCGGCGGATGCTATCCCGGATGTGGCACATTCGTTAGCTTATTAAGTAAATCATTAAGGTGACTTAGTGGACAAAGTTAATAAGATCGCCAAAC

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 79 nt. 2) Cytosine(C) in the sequence= 29 nt. 3) Guanine(G) in the sequence= 46 nt. 4) Thiamine(T) in the sequence= 64 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 218 nt. 8) CG percentage of the sequence= 34.40% 9) *Melting temperature of the DNA based on the Wallace formula= 75.92oC 10) The entered DNA sequence(5-3) is-218 nt.: TTAATAATTAAAGCGCCTGTGCAAAATACCTAAATAGTTATCAAGTATTAAAAGTTAAAATAGTAGAACTTTTATAGATAACGATTTGGATTTTGTAGACGAGGAGGATAGTGATCGAATCAGATCGGCGGATGCTATCCCGGATGTGGCACATTCGTTAGCTTATTAAGTAAATCATTAAGGTGACTTAGTGGACAAAGTTAATAAGATCGCCAAAC 11) The complementary(Com) sequence(3-5) is-218 nt.: AATTATTAATTTCGCGGACACGTTTTATGGATTTATCAATAGTTCATAATTTTCAATTTTATCATCTTGAAAATATCTATTGCTAAACCTAAAACATCTGCTCCTCCTATCACTAGCTTAGTCTAGCCGCCTACGATAGGGCCTACACCGTGTAAGCAATCGAATAATTCATTTAGTAATTCCACTGAATCACCTGTTTCAATTATTCTAGCGGTTTG 12) The reverse(Rev) sequence(3-5) is-218 nt.: CAAACCGCTAGAATAATTGAAACAGGTGATTCAGTGGAATTACTAAATGAATTATTCGATTGCTTACACGGTGTAGGCCCTATCGTAGGCGGCTAGACTAAGCTAGTGATAGGAGGAGCAGATGTTTTAGGTTTAGCAATAGATATTTTCAAGATGATAAAATTGAAAATTATGAACTATTGATAAATCCATAAAACGTGTCCGCGAAATTAATAATT 13) The RevCom sequence(5-3) is-218 nt.: GTTTGGCGATCTTATTAACTTTGTCCACTAAGTCACCTTAATGATTTACTTAATAAGCTAACGAATGTGCCACATCCGGGATAGCATCCGCCGATCTGATTCGATCACTATCCTCCTCGTCTACAAAATCCAAATCGTTATCTATAAAAGTTCTACTATTTTAACTTTTAATACTTGATAACTATTTAGGTATTTTGCACAGGCGCTTTAATTATTAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-119 nt.: TTAATAATTAAAGCGCCTGTGCAAAATACCTAAATAGTTATCAAGTATTAAAAGTTAAAATAGTAGAACTTTTATAGATAACGATTTGGATTTTGTAGACGAGGAGGATAGTGATCGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-119 nt.: GTTTGGCGATCTTATTAACTTTGTCCACTAAGTCACCTTAATGATTTACTTAATAAGCTAACGAATGTGCCACATCCGGGATAGCATCCGCCGATCTGATTCGATCACTATCCTCCTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -52.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -55.37 kcal/mol. The frequency of the MFE structure in the ensemble is 1.12 %. The ensemble diversity is 17.48 The centroid secondary structure in dot-bracket notation with a minimum free energy of -52.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis, GlmS type switch.

2D_Structure (A) (B)

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

StS015305

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RiboSwitch type

GlmS type switch

Bacteria strain target

Staphylococcuss saprophyticus ATCC_15305

Length of Switch in nucleotides

216

Sequence

AGTTCAATTAAAGCGCCTGTACAAGTGAAGAGGTTATGTGTTTGTAATTTAAGGTTTATAACAGAAATCTTAATAGACACGATAATCGAAGTTTGTAGACGAGGAGGGTAGTTATCGAACCATCGGCGGATGCTATCCCGGATGTGGCTCATTCGTTAACTTATTAAGGAAAACATTAGGGTAACCTGGTGCACAAAGTTAATAAGATAGCCAAAA

Above is displayed the nucleotide sequence of the Staphylococcuss saprophyticus ATCC_15305, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 74 nt. 2) Cytosine(C) in the sequence= 31 nt. 3) Guanine(G) in the sequence= 51 nt. 4) Thiamine(T) in the sequence= 60 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 216 nt. 8) CG percentage of the sequence= 37.96% 9) *Melting temperature of the DNA based on the Wallace formula= 77.35oC 10) The entered DNA sequence(5-3) is-216 nt.: AGTTCAATTAAAGCGCCTGTACAAGTGAAGAGGTTATGTGTTTGTAATTTAAGGTTTATAACAGAAATCTTAATAGACACGATAATCGAAGTTTGTAGACGAGGAGGGTAGTTATCGAACCATCGGCGGATGCTATCCCGGATGTGGCTCATTCGTTAACTTATTAAGGAAAACATTAGGGTAACCTGGTGCACAAAGTTAATAAGATAGCCAAAA 11) The complementary(Com) sequence(3-5) is-216 nt.: TCAAGTTAATTTCGCGGACATGTTCACTTCTCCAATACACAAACATTAAATTCCAAATATTGTCTTTAGAATTATCTGTGCTATTAGCTTCAAACATCTGCTCCTCCCATCAATAGCTTGGTAGCCGCCTACGATAGGGCCTACACCGAGTAAGCAATTGAATAATTCCTTTTGTAATCCCATTGGACCACGTGTTTCAATTATTCTATCGGTTTT 12) The reverse(Rev) sequence(3-5) is-216 nt.: AAAACCGATAGAATAATTGAAACACGTGGTCCAATGGGATTACAAAAGGAATTATTCAATTGCTTACTCGGTGTAGGCCCTATCGTAGGCGGCTACCAAGCTATTGATGGGAGGAGCAGATGTTTGAAGCTAATAGCACAGATAATTCTAAAGACAATATTTGGAATTTAATGTTTGTGTATTGGAGAAGTGAACATGTCCGCGAAATTAACTTGA 13) The RevCom sequence(5-3) is-216 nt.: TTTTGGCTATCTTATTAACTTTGTGCACCAGGTTACCCTAATGTTTTCCTTAATAAGTTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATGGTTCGATAACTACCCTCCTCGTCTACAAACTTCGATTATCGTGTCTATTAAGATTTCTGTTATAAACCTTAAATTACAAACACATAACCTCTTCACTTGTACAGGCGCTTTAATTGAACT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-118 nt.: AGTTCAATTAAAGCGCCTGTACAAGTGAAGAGGTTATGTGTTTGTAATTTAAGGTTTATAACAGAAATCTTAATAGACACGATAATCGAAGTTTGTAGACGAGGAGGGTAGTTATCGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-118 nt.: TTTTGGCTATCTTATTAACTTTGTGCACCAGGTTACCCTAATGTTTTCCTTAATAAGTTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATGGTTCGATAACTACCCTCCTCGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcuss saprophyticus ATCC_15305, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcuss saprophyticus ATCC_15305, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -50.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -54.08 kcal/mol. The frequency of the MFE structure in the ensemble is 0.19 %. The ensemble diversity is 26.24The centroid secondary structure in dot-bracket notation with a minimum free energy of -45.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcuss saprophyticus ATCC_15305, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcuss saprophyticus ATCC_15305, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

CB0047119

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RiboSwitch type

GlmS type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

149

Sequence

TACTAAATCAAAGATTTAGACCATCACTTAAGTTGACGAGGTTGGGGAGTATCGAAACTTCGGCGGGTGCCCCACGGTATTTGCACTACCGTTAACAACTGGCAAAGCTATAAAGTAATTTATAGAACAAATCCAGTTAGGTGTTAAAA

Above is displayed the nucleotide sequence of the Clostridium botulinum, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 51 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 32 nt. 4) Thiamine(T) in the sequence= 39 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 149 nt. 8) CG percentage of the sequence= 39.60% 9) *Melting temperature of the DNA based on the Wallace formula= 76.62oC 10) The entered DNA sequence(5-3) is-149 nt.: TACTAAATCAAAGATTTAGACCATCACTTAAGTTGACGAGGTTGGGGAGTATCGAAACTTCGGCGGGTGCCCCACGGTATTTGCACTACCGTTAACAACTGGCAAAGCTATAAAGTAATTTATAGAACAAATCCAGTTAGGTGTTAAAA 11) The complementary(Com) sequence(3-5) is-149 nt.: ATGATTTAGTTTCTAAATCTGGTAGTGAATTCAACTGCTCCAACCCCTCATAGCTTTGAAGCCGCCCACGGGGTGCCATAAACGTGATGGCAATTGTTGACCGTTTCGATATTTCATTAAATATCTTGTTTAGGTCAATCCACAATTTT 12) The reverse(Rev) sequence(3-5) is-149 nt.: AAAATTGTGGATTGACCTAAACAAGATATTTAATGAAATATCGAAACGGTCAACAATTGCCATCACGTTTATGGCACCCCGTGGGCGGCTTCAAAGCTATGAGGGGTTGGAGCAGTTGAATTCACTACCAGATTTAGAAACTAAATCAT 13) The RevCom sequence(5-3) is-149 nt.: TTTTAACACCTAACTGGATTTGTTCTATAAATTACTTTATAGCTTTGCCAGTTGTTAACGGTAGTGCAAATACCGTGGGGCACCCGCCGAAGTTTCGATACTCCCCAACCTCGTCAACTTAAGTGATGGTCTAAATCTTTGATTTAGTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-85 nt.: TACTAAATCAAAGATTTAGACCATCACTTAAGTTGACGAGGTTGGGGAGTATCGAAACTTCGGCGGGTGCCCCACGGTATTTGCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-85 nt.: TTTTAACACCTAACTGGATTTGTTCTATAAATTACTTTATAGCTTTGCCAGTTGTTAACGGTAGTGCAAATACCGTGGGGCACCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -38.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -40.37 kcal/mol. The frequency of the MFE structure in the ensemble is 4.12%. The ensemble diversity is 16.92 The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

CT0089102

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RiboSwitch type

GlmS type switch

Bacteria strain target

Clostridium tetani

Length of Switch in nucleotides

275

Sequence

TTTTAACACCTGATTGATTTGTACCAAAAATTACTCCTTGGTTTTGTCAATCTTTAACGGTAGTGCAGTACCGTGGGGCACCCGCCGAAGATTCGATACTCCCCATCCTCGTCAACTTAAGTGACACCCCAAATCTGTGATTTGGTTGGTGGAACTTACTCAGACCATAGTCTGAGTTTCATTAATCTTACTCCAAATCTGTGATTTGGTTAGTCGAACTTACTCAGACCATAGTCTGAGTTTCATCACCTAAGTCCTGGCGCTTTATTATATTT

Above is displayed the nucleotide sequence of the Clostridium tetani, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 68 nt. 2) Cytosine(C) in the sequence= 64 nt. 3) Guanine(G) in the sequence= 49 nt. 4) Thiamine(T) in the sequence= 94 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 275 nt. 8) CG percentage of the sequence= 41.09% 9) *Melting temperature of the DNA based on the Wallace formula= 79.30oC 10) The entered DNA sequence(5-3) is-275 nt.: TTTTAACACCTGATTGATTTGTACCAAAAATTACTCCTTGGTTTTGTCAATCTTTAACGGTAGTGCAGTACCGTGGGGCACCCGCCGAAGATTCGATACTCCCCATCCTCGTCAACTTAAGTGACACCCCAAATCTGTGATTTGGTTGGTGGAACTTACTCAGACCATAGTCTGAGTTTCATTAATCTTACTCCAAATCTGTGATTTGGTTAGTCGAACTTACTCAGACCATAGTCTGAGTTTCATCACCTAAGTCCTGGCGCTTTATTATATTT 11) The complementary(Com) sequence(3-5) is-275 nt.: AAAATTGTGGACTAACTAAACATGGTTTTTAATGAGGAACCAAAACAGTTAGAAATTGCCATCACGTCATGGCACCCCGTGGGCGGCTTCTAAGCTATGAGGGGTAGGAGCAGTTGAATTCACTGTGGGGTTTAGACACTAAACCAACCACCTTGAATGAGTCTGGTATCAGACTCAAAGTAATTAGAATGAGGTTTAGACACTAAACCAATCAGCTTGAATGAGTCTGGTATCAGACTCAAAGTAGTGGATTCAGGACCGCGAAATAATATAAA 12) The reverse(Rev) sequence(3-5) is-275 nt.: TTTATATTATTTCGCGGTCCTGAATCCACTACTTTGAGTCTGATACCAGACTCATTCAAGCTGATTGGTTTAGTGTCTAAACCTCATTCTAATTACTTTGAGTCTGATACCAGACTCATTCAAGGTGGTTGGTTTAGTGTCTAAACCCCACAGTGAATTCAACTGCTCCTACCCCTCATAGCTTAGAAGCCGCCCACGGGGTGCCATGACGTGATGGCAATTTCTAACTGTTTTGGTTCCTCATTAAAAACCATGTTTAGTTAGTCCACAATTTT 13) The RevCom sequence(5-3) is-275 nt.: AAATATAATAAAGCGCCAGGACTTAGGTGATGAAACTCAGACTATGGTCTGAGTAAGTTCGACTAACCAAATCACAGATTTGGAGTAAGATTAATGAAACTCAGACTATGGTCTGAGTAAGTTCCACCAACCAAATCACAGATTTGGGGTGTCACTTAAGTTGACGAGGATGGGGAGTATCGAATCTTCGGCGGGTGCCCCACGGTACTGCACTACCGTTAAAGATTGACAAAACCAAGGAGTAATTTTTGGTACAAATCAATCAGGTGTTAAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-148 nt.: TTTTAACACCTGATTGATTTGTACCAAAAATTACTCCTTGGTTTTGTCAATCTTTAACGGTAGTGCAGTACCGTGGGGCACCCGCCGAAGATTCGATACTCCCCATCCTCGTCAACTTAAGTGACACCCCAAATCTGTGATTTGGTTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-148 nt.: AAATATAATAAAGCGCCAGGACTTAGGTGATGAAACTCAGACTATGGTCTGAGTAAGTTCGACTAACCAAATCACAGATTTGGAGTAAGATTAATGAAACTCAGACTATGGTCTGAGTAAGTTCCACCAACCAAATCACAGATTTGGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -80.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -82.97 kcal/mol. The frequency of the MFE structure in the ensemble is 1.54%. The ensemble diversity is 46.61. The centroid secondary structure in dot-bracket notation with a minimum free energy of -78.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

EF1825091

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RiboSwitch type

GlmS type switch

Bacteria strain target

Enterococcus faecium

Length of Switch in nucleotides

148

Sequence

CCTTTTAGGATAGCGCCAGGTCTGTGTAAACAGATGACGAGGAGAGGGTTTATCGAAAGATTCGGCGGATGGCCCTAGGGACTGCACTCTACAGAAAATCCACAAAAAATGTCTGCAAAGATAAAACAAAAGGATTTTCCTGCAGCTG

Above is displayed the nucleotide sequence of the Enterococcus faecium, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 49 nt. 2) Cytosine(C) in the sequence= 29 nt. 3) Guanine(G) in the sequence= 38 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 148 nt. 8) CG percentage of the sequence= 45.27% 9) *Melting temperature of the DNA based on the Wallace formula= 78.92oC 10) The entered DNA sequence(5-3) is-148 nt.: CCTTTTAGGATAGCGCCAGGTCTGTGTAAACAGATGACGAGGAGAGGGTTTATCGAAAGATTCGGCGGATGGCCCTAGGGACTGCACTCTACAGAAAATCCACAAAAAATGTCTGCAAAGATAAAACAAAAGGATTTTCCTGCAGCTG 11) The complementary(Com) sequence(3-5) is-148 nt.: GGAAAATCCTATCGCGGTCCAGACACATTTGTCTACTGCTCCTCTCCCAAATAGCTTTCTAAGCCGCCTACCGGGATCCCTGACGTGAGATGTCTTTTAGGTGTTTTTTACAGACGTTTCTATTTTGTTTTCCTAAAAGGACGTCGAC 12) The reverse(Rev) sequence(3-5) is-148 nt.: GTCGACGTCCTTTTAGGAAAACAAAATAGAAACGTCTGTAAAAAACACCTAAAAGACATCTCACGTCAGGGATCCCGGTAGGCGGCTTAGAAAGCTATTTGGGAGAGGAGCAGTAGACAAATGTGTCTGGACCGCGATAGGATTTTCC 13) The RevCom sequence(5-3) is-148 nt.: CAGCTGCAGGAAAATCCTTTTGTTTTATCTTTGCAGACATTTTTTGTGGATTTTCTGTAGAGTGCAGTCCCTAGGGCCATCCGCCGAATCTTTCGATAAACCCTCTCCTCGTCATCTGTTTACACAGACCTGGCGCTATCCTAAAAGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-84 nt.: CCTTTTAGGATAGCGCCAGGTCTGTGTAAACAGATGACGAGGAGAGGGTTTATCGAAAGATTCGGCGGATGGCCCTAGGGACTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-84 nt.: CAGCTGCAGGAAAATCCTTTTGTTTTATCTTTGCAGACATTTTTTGTGGATTTTCTGTAGAGTGCAGTCCCTAGGGCCATCCGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecium, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecium, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -36.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.82 kcal/mol. The frequency of the MFE structure in the ensemble is 1.22%. The ensemble diversity is 21.20. The centroid secondary structure in dot-bracket notation with a minimum free energy of -30.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecium, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecium, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

CP938271012

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RiboSwitch type

GlmS type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

148

Sequence

TTTAAACACCCAATTGGCTTTGTCCTTAAAATCACTTTTAAGTTTTAACCAATCTTTTACGGTAGTGCTTTACCGTGGGGCATCCGCCGAAAATTCGATACTCCCCAACCTCGTCAACTTAAATTTATTAAGAATCTTAATAAGCATTTTAATCTACTAAAGTTAAATTACTTATTAGTCTATAAATAAAACTTTAAGTTCTGGCGCTTTAATCTATTA

Above is displayed the nucleotide sequence of the Clostridium perfringens, GlmS type switch.

Sequence information and analysis

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium perfringens, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

CD0915473

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RiboSwitch type

GlmS type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

180

Sequence

ACACCTTTCTAAGCGCCAGAACTTAGTTATAGACATAATTATTGAGTAATATAGGAACTAAGTTGACGAGGTCAGAGTTAATCGAATTGTCGGCGGATGCTCTGCGGTGTGTTTACCATCGAAAGACTTCTTTAAATAATAGGAGCAATCCTATGGACAAAGGGAAGCCAAAGTAAACTT

Above is displayed the nucleotide sequence of the Clostridium difficile, GlmS type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 61 nt. 2) Cytosine(C) in the sequence= 30 nt. 3) Guanine(G) in the sequence= 40 nt. 4) Thiamine(T) in the sequence= 49 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 180 nt. 8) CG percentage of the sequence= 38.89% 9) *Melting temperature of the DNA based on the Wallace formula= 77.11oC 10) The entered DNA sequence(5-3) is-180 nt.: ACACCTTTCTAAGCGCCAGAACTTAGTTATAGACATAATTATTGAGTAATATAGGAACTAAGTTGACGAGGTCAGAGTTAATCGAATTGTCGGCGGATGCTCTGCGGTGTGTTTACCATCGAAAGACTTCTTTAAATAATAGGAGCAATCCTATGGACAAAGGGAAGCCAAAGTAAACTT 11) The complementary(Com) sequence(3-5) is-180 nt.: TGTGGAAAGATTCGCGGTCTTGAATCAATATCTGTATTAATAACTCATTATATCCTTGATTCAACTGCTCCAGTCTCAATTAGCTTAACAGCCGCCTACGAGACGCCACACAAATGGTAGCTTTCTGAAGAAATTTATTATCCTCGTTAGGATACCTGTTTCCCTTCGGTTTCATTTGAA 12) The reverse(Rev) sequence(3-5) is-180 nt.: TTCAAATGAAACCGAAGGGAAACAGGTATCCTAACGAGGATAATAAATTTCTTCAGAAAGCTACCATTTGTGTGGCGTCTCGTAGGCGGCTGTTAAGCTAATTGAGACTGGAGCAGTTGAATCAAGGATATAATGAGTTATTAATACAGATATTGATTCAAGACCGCGAATCTTTCCACA 13) The RevCom sequence(5-3) is-180 nt.: AAGTTTACTTTGGCTTCCCTTTGTCCATAGGATTGCTCCTATTATTTAAAGAAGTCTTTCGATGGTAAACACACCGCAGAGCATCCGCCGACAATTCGATTAACTCTGACCTCGTCAACTTAGTTCCTATATTACTCAATAATTATGTCTATAACTAAGTTCTGGCGCTTAGAAAGGTGT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-100 nt.: ACACCTTTCTAAGCGCCAGAACTTAGTTATAGACATAATTATTGAGTAATATAGGAACTAAGTTGACGAGGTCAGAGTTAATCGAATTGTCGGCGGATGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-100 nt.: AAGTTTACTTTGGCTTCCCTTTGTCCATAGGATTGCTCCTATTATTTAAAGAAGTCTTTCGATGGTAAACACACCGCAGAGCATCCGCCGACAATTCGAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile, GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile, GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -36.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -40.95 kcal/mol. The frequency of the MFE structure in the ensemble is 0.14%. The ensemble diversity is 38.35. The centroid secondary structure in dot-bracket notation with a minimum free energy of -32.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile, GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile, GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

BS2001921

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RiboSwitch type

GlmS type switch

Bacteria strain target

Bacillus subtilis

Length of Switch in nucleotides

180

Sequence

CCTATAATTATAGCGCCCGAACTAAGCGCCCGGAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTCGCGGATCCTCCCGGCTGAGTGTGCAGATCACAGCCGTAAGAATTTCTTCAAACCAAGGGGGTGACTCCTTGAACAAAGAGAAATCACATGATCTT

Above is displayed the nucleotide sequence of the Bacillus subtilis , GlmS type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 50 nt. 2) Cytosine(C) in The sequence= 38 nt. 3) Guanine(G) in The sequence= 42 nt. 4) Thiamine(T) in The sequence= 38 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 168 nt. 8) CG percentage of The sequence= 47.62% 9) *Melting temperature of The DNA based on the Wallace formula= 80.42oC 10) The entered DNA sequence(5-3) is-168 nt.: CCTATAATTATAGCGCCCGAACTAAGCGCCCGGAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTCGCGGATCCTCCCGGCTGAGTGTGCAGATCACAGCCGTAAGAATTTCTTCAAACCAAGGGGGTGACTCCTTGAACAAAGAGAAATCACATGATCTT 11) The complementary(Com) sequence(3-5) is-168 nt.: GGATATTAATATCGCGGGCTTGATTCGCGGGCCTTTTTCCGAATCAACTGCTCCTACCTCCAATAGCTTAAAGCGCCTAGGAGGGCCGACTCACACGTCTAGTGTCGGCATTCTTAAAGAAGTTTGGTTCCCCCACTGAGGAACTTGTTTCTCTTTAGTGTACTAGAA 12) The reverse(Rev) sequence(3-5) is-168 nt.: TTCTAGTACACTAAAGAGAAACAAGTTCCTCAGTGGGGGAACCAAACTTCTTTAAGAATGCCGACACTAGACGTGTGAGTCGGCCCTCCTAGGCGCTTTAAGCTATTGGAGGTAGGAGCAGTTGATTCGGAAAAAGGCCCGCGAATCAAGCCCGCGATATTAATATCC 13) The RevCom sequence(5-3) is-168 nt.: AAGATCATGTGATTTCTCTTTGTTCAAGGAGTCACCCCCTTGGTTTGAAGAAATTCTTACGGCTGTGATCTGCACACTCAGCCGGGAGGATCCGCGAAATTCGATAACCTCCATCCTCGTCAACTAAGCCTTTTTCCGGGCGCTTAGTTCGGGCGCTATAATTATAGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-94 nt.: CCTATAATTATAGCGCCCGAACTAAGCGCCCGGAAAAAGGCTTAGTTGACGAGGATGGAGGTTATCGAATTTCGCGGATCCTCCCGGCTGAGTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-94 nt.: AAGATCATGTGATTTCTCTTTGTTCAAGGAGTCACCCCCTTGGTTTGAAGAAATTCTTACGGCTGTGATCTGCACACTCAGCCGGGAGGATCCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis , GlmS type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis , GlmS type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -43.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -47.11 kcal/mol. The frequency of the MFE structure in the ensemble is 0.15 %. The ensemble diversity is 24.75. The centroid secondary structure in dot-bracket notation with a minimum free energy of -40.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis , GlmS type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis , GlmS type switch.

Multiple alignment of the GlmS type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the GlmS type switches involved in.

Multi_resistance strains for the GlmS type switches

RiboSwitch_ID:

AB568230

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Acinetobacter baumannii

Length of Switch in nucleotides

208

Sequence

GGGTAGATAGATGAAACAAGTAGGTCTCCGGACTTCAGCGCCATAATTCATTTATGGACATATTCACCTTCCCACACTACTGCAGTGGTGTAAATCGATTTCGACTTAAAAAATATGCTTTACACTGTTACCGTTGCGGGGGCAGTGCCGGACTTTCACCAGCTTCCCTAAAGCATGAATTGCTTACACTTGCTTCCATTTGAACGCA

Above is displayed the nucleotide sequence of the Acinetobacter baumannii , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 56 nt. 2) Cytosine(C) in The sequence= 50 nt. 3) Guanine(G) in The sequence= 42 nt. 4) Thiamine(T) in The sequence= 60 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 208 nt. 8) CG percentage of The sequence= 44.23% 9) *Melting temperature of The DNA based on the Wallace formula= 79.80oC 10) The entered DNA sequence(5-3) is-208 nt.: GGGTAGATAGATGAAACAAGTAGGTCTCCGGACTTCAGCGCCATAATTCATTTATGGACATATTCACCTTCCCACACTACTGCAGTGGTGTAAATCGATTTCGACTTAAAAAATATGCTTTACACTGTTACCGTTGCGGGGGCAGTGCCGGACTTTCACCAGCTTCCCTAAAGCATGAATTGCTTACACTTGCTTCCATTTGAACGCA 11) The complementary(Com) sequence(3-5) is-208 nt.: CCCATCTATCTACTTTGTTCATCCAGAGGCCTGAAGTCGCGGTATTAAGTAAATACCTGTATAAGTGGAAGGGTGTGATGACGTCACCACATTTAGCTAAAGCTGAATTTTTTATACGAAATGTGACAATGGCAACGCCCCCGTCACGGCCTGAAAGTGGTCGAAGGGATTTCGTACTTAACGAATGTGAACGAAGGTAAACTTGCGT 12) The reverse(Rev) sequence(3-5) is-208 nt.: ACGCAAGTTTACCTTCGTTCACATTCGTTAAGTACGAAATCCCTTCGACCACTTTCAGGCCGTGACGGGGGCGTTGCCATTGTCACATTTCGTATAAAAAATTCAGCTTTAGCTAAATGTGGTGACGTCATCACACCCTTCCACTTATACAGGTATTTACTTAATACCGCGACTTCAGGCCTCTGGATGAACAAAGTAGATAGATGGG 13) The RevCom sequence(5-3) is-208 nt.: TGCGTTCAAATGGAAGCAAGTGTAAGCAATTCATGCTTTAGGGAAGCTGGTGAAAGTCCGGCACTGCCCCCGCAACGGTAACAGTGTAAAGCATATTTTTTAAGTCGAAATCGATTTACACCACTGCAGTAGTGTGGGAAGGTGAATATGTCCATAAATGAATTATGGCGCTGAAGTCCGGAGACCTACTTGTTTCATCTATCTACCC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-114 nt.: GGGTAGATAGATGAAACAAGTAGGTCTCCGGACTTCAGCGCCATAATTCATTTATGGACATATTCACCTTCCCACACTACTGCAGTGGTGTAAATCGATTTCGACTTAAAAAAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-114 nt.: TGCGTTCAAATGGAAGCAAGTGTAAGCAATTCATGCTTTAGGGAAGCTGGTGAAAGTCCGGCACTGCCCCCGCAACGGTAACAGTGTAAAGCATATTTTTTAAGTCGAAATCGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Acinetobacter baumannii , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Acinetobacter baumannii , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -46.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -51.16 kcal/mol. The frequency of the MFE structure in the ensemble is 0.03%. The ensemble diversity is 42.11. The centroid secondary structure in dot-bracket notation with a minimum free energy of -41.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Acinetobacter baumannii , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Acinetobacter baumannii , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Below is presented the sequences alignment of all the Cobalamin type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Cobalamin type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Cobalamin riboswitches and shorter motifs based on the general one: 1) N{0,18}GGTYYYN{0,12}RRRYN?AAN{0,2}GGGAAN{0,2}YGGTGN?RAN{0,2}CCRN{0,2}RCN?GYN?CCCGCN?ACTGYRARYGRN?RRN{0,14}GCCACTGRN{0,10}YYGGGAAGGYN{0,10}RN{0,5}YCRYRAGYCAGGAGACCYGCCN{0,18} 2) YCRYRAGYCAGGAGACCYGCC Motifs identified amongst the Cobalamin riboswitches based on the sequences alignment: 1) CNKNHS Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

The table displays known human pathogenic bacteria bearing the Cobalamin type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BA0184334

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

189

Sequence

CCTTTCAAAAGGAAAATAGGTACACGAACATTTCGTTTCGTGTTTAAAAGGGAAGCTTGGTGAAACTCCAACACGGTCCCGCCACTGTAAATGCTGAGATTTCTTTTTGATACCACTGTGAAAACGGGAAGGTAAAAGAAATTATATGAAGCATAAGTCAGGAGACCTGCCTGTTTTAACAACACTGAT

Above is displayed the nucleotide sequence of the Bacillus anthracis , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 64 nt. 2) Cytosine(C) in The sequence= 35 nt. 3) Guanine(G) in The sequence= 40 nt. 4) Thiamine(T) in The sequence= 50 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 189 nt. 8) CG percentage of The sequence= 39.68% 9) *Melting temperature of The DNA based on the Wallace formula= 77.61oC 10) The entered DNA sequence(5-3) is-189 nt.: CCTTTCAAAAGGAAAATAGGTACACGAACATTTCGTTTCGTGTTTAAAAGGGAAGCTTGGTGAAACTCCAACACGGTCCCGCCACTGTAAATGCTGAGATTTCTTTTTGATACCACTGTGAAAACGGGAAGGTAAAAGAAATTATATGAAGCATAAGTCAGGAGACCTGCCTGTTTTAACAACACTGAT 11) The complementary(Com) sequence(3-5) is-189 nt.: GGAAAGTTTTCCTTTTATCCATGTGCTTGTAAAGCAAAGCACAAATTTTCCCTTCGAACCACTTTGAGGTTGTGCCAGGGCGGTGACATTTACGACTCTAAAGAAAAACTATGGTGACACTTTTGCCCTTCCATTTTCTTTAATATACTTCGTATTCAGTCCTCTGGACGGACAAAATTGTTGTGACTA 12) The reverse(Rev) sequence(3-5) is-189 nt.: TAGTCACAACAATTTTGTCCGTCCAGAGGACTGAATACGAAGTATATTAAAGAAAATGGAAGGGCAAAAGTGTCACCATAGTTTTTCTTTAGAGTCGTAAATGTCACCGCCCTGGCACAACCTCAAAGTGGTTCGAAGGGAAAATTTGTGCTTTGCTTTACAAGCACATGGATAAAAGGAAAACTTTCC 13) The RevCom sequence(5-3) is-189 nt.: ATCAGTGTTGTTAAAACAGGCAGGTCTCCTGACTTATGCTTCATATAATTTCTTTTACCTTCCCGTTTTCACAGTGGTATCAAAAAGAAATCTCAGCATTTACAGTGGCGGGACCGTGTTGGAGTTTCACCAAGCTTCCCTTTTAAACACGAAACGAAATGTTCGTGTACCTATTTTCCTTTTGAAAGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-105 nt.: CCTTTCAAAAGGAAAATAGGTACACGAACATTTCGTTTCGTGTTTAAAAGGGAAGCTTGGTGAAACTCCAACACGGTCCCGCCACTGTAAATGCTGAGATTTCTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-105 nt.: ATCAGTGTTGTTAAAACAGGCAGGTCTCCTGACTTATGCTTCATATAATTTCTTTTACCTTCCCGTTTTCACAGTGGTATCAAAAAGAAATCTCAGCATTTACAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -43.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -47.69 kcal/mol. The frequency of the MFE structure in the ensemble is 0.21%. The ensemble diversity is 25.88. The centroid secondary structure in dot-bracket notation with a minimum free energy of -41.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

BC023733

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Bacillus cereus

Length of Switch in nucleotides

191

Sequence

ATCAGTGTTGTTAAAATAGGCAGGTCTCCTGGCTTATGCTTTATACGATTTCTTTCACCTTCCCGTTTTTCACAGTGGTATAGAAAAGAAGTCTCTGCACTTACAGTGGCGGGACCGCGTTGGAATTTCACCAAGCTTCCCTTTTAAACACGAAATAAAAAATTTCGGGTACCTATTTTCCTTTATGAAAG

Above is displayed the nucleotide sequence of the Bacillus cereus , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 51 nt. 2) Cytosine(C) in The sequence= 40 nt. 3) Guanine(G) in The sequence= 36 nt. 4) Thiamine(T) in The sequence= 64 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 191 nt. 8) CG percentage of The sequence= 39.79% 9) *Melting temperature of The DNA based on the Wallace formula= 77.69oC 10) The entered DNA sequence(5-3) is-191 nt.: ATCAGTGTTGTTAAAATAGGCAGGTCTCCTGGCTTATGCTTTATACGATTTCTTTCACCTTCCCGTTTTTCACAGTGGTATAGAAAAGAAGTCTCTGCACTTACAGTGGCGGGACCGCGTTGGAATTTCACCAAGCTTCCCTTTTAAACACGAAATAAAAAATTTCGGGTACCTATTTTCCTTTATGAAAG 11) The complementary(Com) sequence(3-5) is-191 nt.: TAGTCACAACAATTTTATCCGTCCAGAGGACCGAATACGAAATATGCTAAAGAAAGTGGAAGGGCAAAAAGTGTCACCATATCTTTTCTTCAGAGACGTGAATGTCACCGCCCTGGCGCAACCTTAAAGTGGTTCGAAGGGAAAATTTGTGCTTTATTTTTTAAAGCCCATGGATAAAAGGAAATACTTTC 12) The reverse(Rev) sequence(3-5) is-191 nt.: GAAAGTATTTCCTTTTATCCATGGGCTTTAAAAAATAAAGCACAAATTTTCCCTTCGAACCACTTTAAGGTTGCGCCAGGGCGGTGACATTCACGTCTCTGAAGAAAAGATATGGTGACACTTTTTGCCCTTCCACTTTCTTTAGCATATTTCGTATTCGGTCCTCTGGACGGATAAAATTGTTGTGACTA 13) The RevCom sequence(5-3) is-191 nt.: CTTTCATAAAGGAAAATAGGTACCCGAAATTTTTTATTTCGTGTTTAAAAGGGAAGCTTGGTGAAATTCCAACGCGGTCCCGCCACTGTAAGTGCAGAGACTTCTTTTCTATACCACTGTGAAAAACGGGAAGGTGAAAGAAATCGTATAAAGCATAAGCCAGGAGACCTGCCTATTTTAACAACACTGAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-106 nt.: ATCAGTGTTGTTAAAATAGGCAGGTCTCCTGGCTTATGCTTTATACGATTTCTTTCACCTTCCCGTTTTTCACAGTGGTATAGAAAAGAAGTCTCTGCACTTACAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-106 nt.: CTTTCATAAAGGAAAATAGGTACCCGAAATTTTTTATTTCGTGTTTAAAAGGGAAGCTTGGTGAAATTCCAACGCGGTCCCGCCACTGTAAGTGCAGAGACTTCTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus cereus , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus cereus , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus cereus , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus cereus , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

BT452848

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Bordetella pertussis strain Tohama I

Length of Switch in nucleotides

160

Sequence

CAGTTCTGGCCCCGAACCGGTGCTTTCGGCAAGTACGCTTGCGCGGAAGGTAAACGGGAAACAGGAAGGCCCTGCCCAGCCTGTGCTGCCCCCGCAACGGTCCCCATGGCGCGCGACGCGCCGTGGCAGCCCGATACCGGCCGGTTCGACAGCGAGGATG

Above is displayed the nucleotide sequence of the Bordetella pertussis strain Tohama I, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 29 nt. 2) Cytosine(C) in The sequence= 55 nt. 3) Guanine(G) in The sequence= 54 nt. 4) Thiamine(T) in The sequence= 22 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 160 nt. 8) CG percentage of The sequence= 68.12% 9) *Melting temperature of The DNA based on the Wallace formula= 88.63oC 10) The entered DNA sequence(5-3) is-160 nt.: CAGTTCTGGCCCCGAACCGGTGCTTTCGGCAAGTACGCTTGCGCGGAAGGTAAACGGGAAACAGGAAGGCCCTGCCCAGCCTGTGCTGCCCCCGCAACGGTCCCCATGGCGCGCGACGCGCCGTGGCAGCCCGATACCGGCCGGTTCGACAGCGAGGATG 11) The complementary(Com) sequence(3-5) is-160 nt.: GTCAAGACCGGGGCTTGGCCACGAAAGCCGTTCATGCGAACGCGCCTTCCATTTGCCCTTTGTCCTTCCGGGACGGGTCGGACACGACGGGGGCGTTGCCAGGGGTACCGCGCGCTGCGCGGCACCGTCGGGCTATGGCCGGCCAAGCTGTCGCTCCTAC 12) The reverse(Rev) sequence(3-5) is-160 nt.: GTAGGAGCGACAGCTTGGCCGGCCATAGCCCGACGGTGCCGCGCAGCGCGCGGTACCCCTGGCAACGCCCCCGTCGTGTCCGACCCGTCCCGGAAGGACAAAGGGCAAATGGAAGGCGCGTTCGCATGAACGGCTTTCGTGGCCAAGCCCCGGTCTTGAC 13) The RevCom sequence(5-3) is-160 nt.: CATCCTCGCTGTCGAACCGGCCGGTATCGGGCTGCCACGGCGCGTCGCGCGCCATGGGGACCGTTGCGGGGGCAGCACAGGCTGGGCAGGGCCTTCCTGTTTCCCGTTTACCTTCCGCGCAAGCGTACTTGCCGAAAGCACCGGTTCGGGGCCAGAACTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-90 nt.: CAGTTCTGGCCCCGAACCGGTGCTTTCGGCAAGTACGCTTGCGCGGAAGGTAAACGGGAAACAGGAAGGCCCTGCCCAGCCTGTGCTGCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-90 nt.: CATCCTCGCTGTCGAACCGGCCGGTATCGGGCTGCCACGGCGCGTCGCGCGCCATGGGGACCGTTGCGGGGGCAGCACAGGCTGGGCAGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bordetella pertussis strain Tohama I, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bordetella pertussis strain Tohama I, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -76.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -76.66 kcal/mol. The frequency of the MFE structure in the ensemble is 40.06%. The ensemble diversity is 10.19. The centroid secondary structure in dot-bracket notation with a minimum free energy of -76.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bordetella pertussis strain Tohama I, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bordetella pertussis strain Tohama I, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

BM573400

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Brucella melitensis biovar Abortus

Length of Switch in nucleotides

233

Sequence

CCGTAATACCGTCATGACGGTTCCCCGACCGAGAGCGAAGGGGATTAATAGGGAACACGGTGAGGACGACCCATCAAGGGGCCGAGACCGTGGCTGCCCCCGCAACTGTAAGCGGATTGCCGTTCATCCTCGTGACGCCGAAAGCGTCATGCCACTGTGCCCACGGCACGGGAAGGCAGATGGACGGCGATTATCCGCAAGCCAGGAGACCTGCCGTCTTACGTAGTCCATTG

Above is displayed the nucleotide sequence of the Brucella melitensis biovar Abortus , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 54 nt. 2) Cytosine(C) in The sequence= 69 nt. 3) Guanine(G) in The sequence= 72 nt. 4) Thiamine(T) in The sequence= 38 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 233 nt. 8) CG percentage of The sequence= 60.52% 9) *Melting temperature of The DNA based on the Wallace formula= 86.83oC 10) The entered DNA sequence(5-3) is-233 nt.: CCGTAATACCGTCATGACGGTTCCCCGACCGAGAGCGAAGGGGATTAATAGGGAACACGGTGAGGACGACCCATCAAGGGGCCGAGACCGTGGCTGCCCCCGCAACTGTAAGCGGATTGCCGTTCATCCTCGTGACGCCGAAAGCGTCATGCCACTGTGCCCACGGCACGGGAAGGCAGATGGACGGCGATTATCCGCAAGCCAGGAGACCTGCCGTCTTACGTAGTCCATTG 11) The complementary(Com) sequence(3-5) is-233 nt.: GGCATTATGGCAGTACTGCCAAGGGGCTGGCTCTCGCTTCCCCTAATTATCCCTTGTGCCACTCCTGCTGGGTAGTTCCCCGGCTCTGGCACCGACGGGGGCGTTGACATTCGCCTAACGGCAAGTAGGAGCACTGCGGCTTTCGCAGTACGGTGACACGGGTGCCGTGCCCTTCCGTCTACCTGCCGCTAATAGGCGTTCGGTCCTCTGGACGGCAGAATGCATCAGGTAAC 12) The reverse(Rev) sequence(3-5) is-233 nt.: GTTACCTGATGCATTCTGCCGTCCAGAGGACCGAACGCCTATTAGCGGCAGGTAGACGGAAGGGCACGGCACCCGTGTCACCGTACTGCGAAAGCCGCAGTGCTCCTACTTGCCGTTAGGCGAATGTCAACGCCCCCGTCGGTGCCAGAGCCGGGGAACTACCCAGCAGGAGTGGCACAAGGGATAATTAGGGGAAGCGAGAGCCAGCCCCTTGGCAGTACTGCCATAATGCC 13) The RevCom sequence(5-3) is-233 nt.: CAATGGACTACGTAAGACGGCAGGTCTCCTGGCTTGCGGATAATCGCCGTCCATCTGCCTTCCCGTGCCGTGGGCACAGTGGCATGACGCTTTCGGCGTCACGAGGATGAACGGCAATCCGCTTACAGTTGCGGGGGCAGCCACGGTCTCGGCCCCTTGATGGGTCGTCCTCACCGTGTTCCCTATTAATCCCCTTCGCTCTCGGTCGGGGAACCGTCATGACGGTATTACGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-127 nt.: CCGTAATACCGTCATGACGGTTCCCCGACCGAGAGCGAAGGGGATTAATAGGGAACACGGTGAGGACGACCCATCAAGGGGCCGAGACCGTGGCTGCCCCCGCAACTGTAAGCGGATTGCCGTTCAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-127 nt.: CAATGGACTACGTAAGACGGCAGGTCTCCTGGCTTGCGGATAATCGCCGTCCATCTGCCTTCCCGTGCCGTGGGCACAGTGGCATGACGCTTTCGGCGTCACGAGGATGAACGGCAATCCGCTTACA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Brucella melitensis biovar Abortus , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Brucella melitensis biovar Abortus , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -92.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -95.25 kcal/mol. The frequency of the MFE structure in the ensemble is 0.71%. The ensemble diversity is 37.81. The centroid secondary structure in dot-bracket notation with a minimum free energy of -79.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Brucella melitensis biovar Abortus , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Brucella melitensis biovar Abortus , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

CB456717

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Clostridium botulinum A str. ATCC 3502

Length of Switch in nucleotides

182

Sequence

ATTTAATAAAAAGATTTAGGTGCCTTTACATAAAAGGTGAAAAGGGAATGTGGTAAAAGCCACAGCAGCCCCCGCTACTGTAATTGAGGACAAATCTTTCATAAACCACTCTTTAAAAAGGGGAAGGGAAAGATTAGGATGAATCATGAGCCAGGAGACCTGCCTAGATTTTTATTAGGGAA

Above is displayed the nucleotide sequence of the Clostridium botulinum A str. ATCC 3502 , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 68 nt. 2) Cytosine(C) in The sequence= 28 nt. 3) Guanine(G) in The sequence= 42 nt. 4) Thiamine(T) in The sequence= 44 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 182 nt. 8) CG percentage of The sequence= 38.46% 9) *Melting temperature of The DNA based on the Wallace formula= 76.97oC 10) The entered DNA sequence(5-3) is-182 nt.: ATTTAATAAAAAGATTTAGGTGCCTTTACATAAAAGGTGAAAAGGGAATGTGGTAAAAGCCACAGCAGCCCCCGCTACTGTAATTGAGGACAAATCTTTCATAAACCACTCTTTAAAAAGGGGAAGGGAAAGATTAGGATGAATCATGAGCCAGGAGACCTGCCTAGATTTTTATTAGGGAA 11) The complementary(Com) sequence(3-5) is-182 nt.: TAAATTATTTTTCTAAATCCACGGAAATGTATTTTCCACTTTTCCCTTACACCATTTTCGGTGTCGTCGGGGGCGATGACATTAACTCCTGTTTAGAAAGTATTTGGTGAGAAATTTTTCCCCTTCCCTTTCTAATCCTACTTAGTACTCGGTCCTCTGGACGGATCTAAAAATAATCCCTT 12) The reverse(Rev) sequence(3-5) is-182 nt.: AAGGGATTATTTTTAGATCCGTCCAGAGGACCGAGTACTAAGTAGGATTAGAAAGGGAAGGGGAAAAATTTCTCACCAAATACTTTCTAAACAGGAGTTAATGTCATCGCCCCCGACGACACCGAAAATGGTGTAAGGGAAAAGTGGAAAATACATTTCCGTGGATTTAGAAAAATAATTTA 13) The RevCom sequence(5-3) is-182 nt.: TTCCCTAATAAAAATCTAGGCAGGTCTCCTGGCTCATGATTCATCCTAATCTTTCCCTTCCCCTTTTTAAAGAGTGGTTTATGAAAGATTTGTCCTCAATTACAGTAGCGGGGGCTGCTGTGGCTTTTACCACATTCCCTTTTCACCTTTTATGTAAAGGCACCTAAATCTTTTTATTAAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-101 nt.: ATTTAATAAAAAGATTTAGGTGCCTTTACATAAAAGGTGAAAAGGGAATGTGGTAAAAGCCACAGCAGCCCCCGCTACTGTAATTGAGGACAAATCTTTCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-101 nt.: TTCCCTAATAAAAATCTAGGCAGGTCTCCTGGCTCATGATTCATCCTAATCTTTCCCTTCCCCTTTTTAAAGAGTGGTTTATGAAAGATTTGTCCTCAATT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum A str. ATCC 3502 , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum A str. ATCC 3502 , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -42.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -47.33 kcal/mol. The frequency of the MFE structure in the ensemble is 0.04%. The ensemble diversity is 32.11. The centroid secondary structure in dot-bracket notation with a minimum free energy of -35.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum A str. ATCC 3502 , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum A str. ATCC 3502 , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

CD3578965

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

182

Sequence

TGAACTTATATAATACTGGGCAGGTCTCCTGACTCACGGCTTTTCCTCCATCACCCTTCCCAAAATTTTTATAAATTTCAGTGGATTTTGATTTCGTATCCGTATACAGTAGCGGGGGCTGTAGTGAATTTTCATCACTTTCCCTATTAAACTAATATAGTACCCTAGTATTATTTTAATTT

Above is displayed the nucleotide sequence of the Clostridium difficile , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 47 nt. 2) Cytosine(C) in The sequence= 38 nt. 3) Guanine(G) in The sequence= 27 nt. 4) Thiamine(T) in The sequence= 70 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 182 nt. 8) CG percentage of The sequence= 35.71% 9) *Melting temperature of The DNA based on the Wallace formula= 75.85oC 10) The entered DNA sequence(5-3) is-182 nt.: TGAACTTATATAATACTGGGCAGGTCTCCTGACTCACGGCTTTTCCTCCATCACCCTTCCCAAAATTTTTATAAATTTCAGTGGATTTTGATTTCGTATCCGTATACAGTAGCGGGGGCTGTAGTGAATTTTCATCACTTTCCCTATTAAACTAATATAGTACCCTAGTATTATTTTAATTT 11) The complementary(Com) sequence(3-5) is-182 nt.: ACTTGAATATATTATGACCCGTCCAGAGGACTGAGTGCCGAAAAGGAGGTAGTGGGAAGGGTTTTAAAAATATTTAAAGTCACCTAAAACTAAAGCATAGGCATATGTCATCGCCCCCGACATCACTTAAAAGTAGTGAAAGGGATAATTTGATTATATCATGGGATCATAATAAAATTAAA 12) The reverse(Rev) sequence(3-5) is-182 nt.: TTTAATTTTATTATGATCCCATGATATAATCAAATTATCCCTTTCACTACTTTTAAGTGATGTCGGGGGCGATGACATATGCCTATGCTTTAGTTTTAGGTGACTTTAAATATTTTTAAAACCCTTCCCACTACCTCCTTTTCGGCACTCAGTCCTCTGGACGGGTCATAATATATTCAAGT 13) The RevCom sequence(5-3) is-182 nt.: AAATTAAAATAATACTAGGGTACTATATTAGTTTAATAGGGAAAGTGATGAAAATTCACTACAGCCCCCGCTACTGTATACGGATACGAAATCAAAATCCACTGAAATTTATAAAAATTTTGGGAAGGGTGATGGAGGAAAAGCCGTGAGTCAGGAGACCTGCCCAGTATTATATAAGTTCA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-101 nt.: TGAACTTATATAATACTGGGCAGGTCTCCTGACTCACGGCTTTTCCTCCATCACCCTTCCCAAAATTTTTATAAATTTCAGTGGATTTTGATTTCGTATCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-101 nt.: AAATTAAAATAATACTAGGGTACTATATTAGTTTAATAGGGAAAGTGATGAAAATTCACTACAGCCCCCGCTACTGTATACGGATACGAAATCAAAATCCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -33.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -37.62 kcal/mol. The frequency of the MFE structure in the ensemble is 0.15 %. The ensemble diversity is 42.50. The centroid secondary structure in dot-bracket notation with a minimum free energy of -21.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile , Cobalamin type switch.

2D_Structure (A) (B)

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

CP46321413

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Clostridium perfringens str.13

Length of Switch in nucleotides

180

Sequence

CTTAGTTCATGATCTTTAGGCAGGTATCCTGACTTAAGGCTTATCCTCATTTCTCCCTTCCCAATTTATATAATCAGTGGTCAAATAGAAACTTGTATCCTATCACAGTAGCGGGGGCTGTAGTGGACTTTAACCACTTTCCCTTTTAATTAAAATCAAACCTAAAAATATAAAATATTA

Above is displayed the nucleotide sequence of the Clostridium perfringens str.13 , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 56 nt. 2) Cytosine(C) in The sequence= 37 nt. 3) Guanine(G) in The sequence= 25 nt. 4) Thiamine(T) in The sequence= 62 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 180 nt. 8) CG percentage of The sequence= 34.44% 9) *Melting temperature of The DNA based on the Wallace formula= 75.29oC 10) The entered DNA sequence(5-3) is-180 nt.: CTTAGTTCATGATCTTTAGGCAGGTATCCTGACTTAAGGCTTATCCTCATTTCTCCCTTCCCAATTTATATAATCAGTGGTCAAATAGAAACTTGTATCCTATCACAGTAGCGGGGGCTGTAGTGGACTTTAACCACTTTCCCTTTTAATTAAAATCAAACCTAAAAATATAAAATATTA 11) The complementary(Com) sequence(3-5) is-180 nt.: GAATCAAGTACTAGAAATCCGTCCATAGGACTGAATTCCGAATAGGAGTAAAGAGGGAAGGGTTAAATATATTAGTCACCAGTTTATCTTTGAACATAGGATAGTGTCATCGCCCCCGACATCACCTGAAATTGGTGAAAGGGAAAATTAATTTTAGTTTGGATTTTTATATTTTATAAT 12) The reverse(Rev) sequence(3-5) is-180 nt.: ATTATAAAATATAAAAATCCAAACTAAAATTAATTTTCCCTTTCACCAATTTCAGGTGATGTCGGGGGCGATGACACTATCCTATGTTCAAAGATAAACTGGTGACTAATATATTTAACCCTTCCCTCTTTACTCCTATTCGGAATTCAGTCCTATGGACGGATTTCTAGTACTTGATTC 13) The RevCom sequence(5-3) is-180 nt.: TAATATTTTATATTTTTAGGTTTGATTTTAATTAAAAGGGAAAGTGGTTAAAGTCCACTACAGCCCCCGCTACTGTGATAGGATACAAGTTTCTATTTGACCACTGATTATATAAATTGGGAAGGGAGAAATGAGGATAAGCCTTAAGTCAGGATACCTGCCTAAAGATCATGAACTAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-100 nt.: CTTAGTTCATGATCTTTAGGCAGGTATCCTGACTTAAGGCTTATCCTCATTTCTCCCTTCCCAATTTATATAATCAGTGGTCAAATAGAAACTTGTATCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-100 nt.: TAATATTTTATATTTTTAGGTTTGATTTTAATTAAAAGGGAAAGTGGTTAAAGTCCACTACAGCCCCCGCTACTGTGATAGGATACAAGTTTCTATTTGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens str.13 , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens str.13 , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -26.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -29.97 kcal/mol. The frequency of the MFE structure in the ensemble is 0.36 %. The ensemble diversity is 37.11. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens str.13 , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium perfringens str.13 , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

CT534001

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Clostridium tetani E88

Length of Switch in nucleotides

184

Sequence

CATATTATGAATTTTTATGGTGTAATTTCACATTACGTAAAAGGGAAGCTTGGTGTAAATCCAGCACGGTCCCGCCACTGTAAGAGAGAGTATATCATTATATGCCACTGTTGTTTATCAATGGGAAGGCAATGATGTACTATGATCTCAAGTCAGGAGACCTACCATAAAAACTTATACAATT

Above is displayed the nucleotide sequence of the Clostridium tetani E88, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 61 nt. 2) Cytosine(C) in The sequence= 31 nt. 3) Guanine(G) in The sequence= 36 nt. 4) Thiamine(T) in The sequence= 56 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 184 nt. 8) CG percentage of The sequence= 36.41% 9) *Melting temperature of The DNA based on the Wallace formula= 76.18oC 10) The entered DNA sequence(5-3) is-184 nt.: CATATTATGAATTTTTATGGTGTAATTTCACATTACGTAAAAGGGAAGCTTGGTGTAAATCCAGCACGGTCCCGCCACTGTAAGAGAGAGTATATCATTATATGCCACTGTTGTTTATCAATGGGAAGGCAATGATGTACTATGATCTCAAGTCAGGAGACCTACCATAAAAACTTATACAATT 11) The complementary(Com) sequence(3-5) is-184 nt.: GTATAATACTTAAAAATACCACATTAAAGTGTAATGCATTTTCCCTTCGAACCACATTTAGGTCGTGCCAGGGCGGTGACATTCTCTCTCATATAGTAATATACGGTGACAACAAATAGTTACCCTTCCGTTACTACATGATACTAGAGTTCAGTCCTCTGGATGGTATTTTTGAATATGTTAA 12) The reverse(Rev) sequence(3-5) is-184 nt.: TTAACATATTCAAAAATACCATCCAGAGGACTGAACTCTAGTATCATGTAGTAACGGAAGGGTAACTATTTGTTGTCACCGTATATTACTATATGAGAGAGAATGTCACCGCCCTGGCACGACCTAAATGTGGTTCGAAGGGAAAATGCATTACACTTTAATGTGGTATTTTTAAGTATTATAC 13) The RevCom sequence(5-3) is-184 nt.: AATTGTATAAGTTTTTATGGTAGGTCTCCTGACTTGAGATCATAGTACATCATTGCCTTCCCATTGATAAACAACAGTGGCATATAATGATATACTCTCTCTTACAGTGGCGGGACCGTGCTGGATTTACACCAAGCTTCCCTTTTACGTAATGTGAAATTACACCATAAAAATTCATAATATG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-102 nt.: CATATTATGAATTTTTATGGTGTAATTTCACATTACGTAAAAGGGAAGCTTGGTGTAAATCCAGCACGGTCCCGCCACTGTAAGAGAGAGTATATCATTATA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-102 nt.: AATTGTATAAGTTTTTATGGTAGGTCTCCTGACTTGAGATCATAGTACATCATTGCCTTCCCATTGATAAACAACAGTGGCATATAATGATATACTCTCTCT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani E88, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani E88, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -49.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -51.33 kcal/mol. The frequency of the MFE structure in the ensemble is 4.36 %. The ensemble diversity is 22.07. The centroid secondary structure in dot-bracket notation with a minimum free energy of -45.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani E88, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani E88, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

NCT245743

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Corynebacterium diphtheriae NCTC 13129

Length of Switch in nucleotides

201

Sequence

TGTGTTACACATTGATTAGGTGCAGCATAGAACTGCTGCATGGGAATCTGGTGAAAATCCAGAGCTGACGCGCAGCGGTGAAGGTGCAAGTGAGTGCTTCAATGTAGCCACTGAGAGTATAAAAACTCTTGGGAAGGTGAGGCAATTACTCTCGCGTAGAGCACCCCAGTCCGAAGACCGGCCTAATCAGAAACATGTGCT

Above is displayed the nucleotide sequence of the Corynebacterium diphtheriae NCTC 13129, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 58 nt. 2) Cytosine(C) in The sequence= 42 nt. 3) Guanine(G) in The sequence= 57 nt. 4) Thiamine(T) in The sequence= 44 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 201 nt. 8) CG percentage of The sequence= 49.25% 9) *Melting temperature of The DNA based on the Wallace formula= 81.75oC 10) The entered DNA sequence(5-3) is-201 nt.: TGTGTTACACATTGATTAGGTGCAGCATAGAACTGCTGCATGGGAATCTGGTGAAAATCCAGAGCTGACGCGCAGCGGTGAAGGTGCAAGTGAGTGCTTCAATGTAGCCACTGAGAGTATAAAAACTCTTGGGAAGGTGAGGCAATTACTCTCGCGTAGAGCACCCCAGTCCGAAGACCGGCCTAATCAGAAACATGTGCT 11) The complementary(Com) sequence(3-5) is-201 nt.: ACACAATGTGTAACTAATCCACGTCGTATCTTGACGACGTACCCTTAGACCACTTTTAGGTCTCGACTGCGCGTCGCCACTTCCACGTTCACTCACGAAGTTACATCGGTGACTCTCATATTTTTGAGAACCCTTCCACTCCGTTAATGAGAGCGCATCTCGTGGGGTCAGGCTTCTGGCCGGATTAGTCTTTGTACACGA 12) The reverse(Rev) sequence(3-5) is-201 nt.: TCGTGTACAAAGACTAATCCGGCCAGAAGCCTGACCCCACGAGATGCGCTCTCATTAACGGAGTGGAAGGGTTCTCAAAAATATGAGAGTCACCGATGTAACTTCGTGAGTGAACGTGGAAGTGGCGACGCGCAGTCGAGACCTAAAAGTGGTCTAAGGGTACGTCGTCAAGATACGACGTGGATTAGTTACACATTGTGT 13) The RevCom sequence(5-3) is-201 nt.: AGCACATGTTTCTGATTAGGCCGGTCTTCGGACTGGGGTGCTCTACGCGAGAGTAATTGCCTCACCTTCCCAAGAGTTTTTATACTCTCAGTGGCTACATTGAAGCACTCACTTGCACCTTCACCGCTGCGCGTCAGCTCTGGATTTTCACCAGATTCCCATGCAGCAGTTCTATGCTGCACCTAATCAATGTGTAACACA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-111 nt.: TGTGTTACACATTGATTAGGTGCAGCATAGAACTGCTGCATGGGAATCTGGTGAAAATCCAGAGCTGACGCGCAGCGGTGAAGGTGCAAGTGAGTGCTTCAATGTAGCCAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-111 nt.: AGCACATGTTTCTGATTAGGCCGGTCTTCGGACTGGGGTGCTCTACGCGAGAGTAATTGCCTCACCTTCCCAAGAGTTTTTATACTCTCAGTGGCTACATTGAAGCACTCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Corynebacterium diphtheriae NCTC 13129, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Corynebacterium diphtheriae NCTC 13129, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -67.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -70.37 kcal/mol. The frequency of the MFE structure in the ensemble is 1.31 %. The ensemble diversity is 35.21. The centroid secondary structure in dot-bracket notation with a minimum free energy of -58.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Corynebacterium diphtheriae NCTC 13129, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Corynebacterium diphtheriae NCTC 13129, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

EF3124668

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Enterococcus faecalis V583

Length of Switch in nucleotides

172

Sequence

GAATGATTAGACTTATCAAGCCGGTATCCTGACTTAGCTTCTTCTTACTCCCAATCCTTCCAGAATAATCTGTGGTCTTATTGGTTTCATCCACCATACAGTAGGTAGGTCTGTAGAGGATTCGCACCTCTTTCCCTGACACTTCATAAGTACATATATATTGTATCTTCGT

Above is displayed the nucleotide sequence of the Enterococcus faecalis V583 , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 42 nt. 2) Cytosine(C) in The sequence= 41 nt. 3) Guanine(G) in The sequence= 28 nt. 4) Thiamine(T) in The sequence= 61 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 172 nt. 8) CG percentage of The sequence= 40.12% 9) *Melting temperature of The DNA based on the Wallace formula= 77.44oC 10) The entered DNA sequence(5-3) is-172 nt.: GAATGATTAGACTTATCAAGCCGGTATCCTGACTTAGCTTCTTCTTACTCCCAATCCTTCCAGAATAATCTGTGGTCTTATTGGTTTCATCCACCATACAGTAGGTAGGTCTGTAGAGGATTCGCACCTCTTTCCCTGACACTTCATAAGTACATATATATTGTATCTTCGT 11) The complementary(Com) sequence(3-5) is-172 nt.: CTTACTAATCTGAATAGTTCGGCCATAGGACTGAATCGAAGAAGAATGAGGGTTAGGAAGGTCTTATTAGACACCAGAATAACCAAAGTAGGTGGTATGTCATCCATCCAGACATCTCCTAAGCGTGGAGAAAGGGACTGTGAAGTATTCATGTATATATAACATAGAAGCA 12) The reverse(Rev) sequence(3-5) is-172 nt.: TGCTTCTATGTTATATATACATGAATACTTCACAGTCCCTTTCTCCACGCTTAGGAGATGTCTGGATGGATGACATACCACCTACTTTGGTTATTCTGGTGTCTAATAAGACCTTCCTAACCCTCATTCTTCTTCGATTCAGTCCTATGGCCGAACTATTCAGATTAGTAAG 13) The RevCom sequence(5-3) is-172 nt.: ACGAAGATACAATATATATGTACTTATGAAGTGTCAGGGAAAGAGGTGCGAATCCTCTACAGACCTACCTACTGTATGGTGGATGAAACCAATAAGACCACAGATTATTCTGGAAGGATTGGGAGTAAGAAGAAGCTAAGTCAGGATACCGGCTTGATAAGTCTAATCATTC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-96 nt.: GAATGATTAGACTTATCAAGCCGGTATCCTGACTTAGCTTCTTCTTACTCCCAATCCTTCCAGAATAATCTGTGGTCTTATTGGTTTCATCCACCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-96 nt.: ACGAAGATACAATATATATGTACTTATGAAGTGTCAGGGAAAGAGGTGCGAATCCTCTACAGACCTACCTACTGTATGGTGGATGAAACCAATAAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecalis V583 , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecalis V583 , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -27.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -30.99 kcal/mol. The frequency of the MFE structure in the ensemble is 0.18 %. The ensemble diversity is 35.79. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecalis V583 , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecalis V583 , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

KMG387549

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Klebsiella pneumoniae subsp. pneumoniae MGH 78578

Length of Switch in nucleotides

188

Sequence

TTGTAGCATTCGCCTACCGGTCCTGTGAGTTAAAAGGGAACCCAGTGGAAATCTGGGGCTGACGCGCAGCGGTAAGGAAGGTGAGAAATGAGCGCACTCGGTGCAGACACTGCGGCTAGCCGTGGGAAGTCATTATTTCTTGAAACAGCCTCCAAGCCCGAAGACCTGCCGGAATACGTCGCACTGGG

Above is displayed the nucleotide sequence of the Klebsiella pneumoniae subsp. pneumoniae MGH 78578, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 47 nt. 2) Cytosine(C) in The sequence= 46 nt. 3) Guanine(G) in The sequence= 59 nt. 4) Thiamine(T) in The sequence= 36 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 188 nt. 8) CG percentage of The sequence= 55.85% 9) *Melting temperature of The DNA based on the Wallace formula= 84.22oC 10) The entered DNA sequence(5-3) is-188 nt.: TTGTAGCATTCGCCTACCGGTCCTGTGAGTTAAAAGGGAACCCAGTGGAAATCTGGGGCTGACGCGCAGCGGTAAGGAAGGTGAGAAATGAGCGCACTCGGTGCAGACACTGCGGCTAGCCGTGGGAAGTCATTATTTCTTGAAACAGCCTCCAAGCCCGAAGACCTGCCGGAATACGTCGCACTGGG 11) The complementary(Com) sequence(3-5) is-188 nt.: AACATCGTAAGCGGATGGCCAGGACACTCAATTTTCCCTTGGGTCACCTTTAGACCCCGACTGCGCGTCGCCATTCCTTCCACTCTTTACTCGCGTGAGCCACGTCTGTGACGCCGATCGGCACCCTTCAGTAATAAAGAACTTTGTCGGAGGTTCGGGCTTCTGGACGGCCTTATGCAGCGTGACCC 12) The reverse(Rev) sequence(3-5) is-188 nt.: GGGTCACGCTGCATAAGGCCGTCCAGAAGCCCGAACCTCCGACAAAGTTCTTTATTACTGAAGGGTGCCGATCGGCGTCACAGACGTGGCTCACGCGAGTAAAGAGTGGAAGGAATGGCGACGCGCAGTCGGGGTCTAAAGGTGACCCAAGGGAAAATTGAGTGTCCTGGCCATCCGCTTACGATGTT 13) The RevCom sequence(5-3) is-188 nt.: CCCAGTGCGACGTATTCCGGCAGGTCTTCGGGCTTGGAGGCTGTTTCAAGAAATAATGACTTCCCACGGCTAGCCGCAGTGTCTGCACCGAGTGCGCTCATTTCTCACCTTCCTTACCGCTGCGCGTCAGCCCCAGATTTCCACTGGGTTCCCTTTTAACTCACAGGACCGGTAGGCGAATGCTACAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-104 nt.: TTGTAGCATTCGCCTACCGGTCCTGTGAGTTAAAAGGGAACCCAGTGGAAATCTGGGGCTGACGCGCAGCGGTAAGGAAGGTGAGAAATGAGCGCACTCGGTGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-104 nt.: CCCAGTGCGACGTATTCCGGCAGGTCTTCGGGCTTGGAGGCTGTTTCAAGAAATAATGACTTCCCACGGCTAGCCGCAGTGTCTGCACCGAGTGCGCTCATTTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Klebsiella pneumoniae subsp. pneumoniae MGH 78578, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Klebsiella pneumoniae subsp. pneumoniae MGH 78578, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -57.34 kcal/mol. The frequency of the MFE structure in the ensemble is 0.72 %. The ensemble diversity is 64.52. The centroid secondary structure in dot-bracket notation with a minimum free energy of -40.99 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Klebsiella pneumoniae subsp. pneumoniae MGH 78578, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Klebsiella pneumoniae subsp. pneumoniae MGH 78578, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

LI4512300

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Leptospira interrogans serovar Lai str. 56601

Length of Switch in nucleotides

181

Sequence

TCTTGGAACGGAAAACTTGTTTATTCTCGTGATGAGGAAGGGAATCCGGTTCAAATCCGGAGCTGAACCCGCAGCTGTAATCGCCGAATGAGATTTCGCAATCATGCCACTGCGTTAAATACGCGGGAAGGCTGCGAAATCGGCGAAAGCCAGAAGACCTAACAAGTAAAAAAACAAACTA

Above is displayed the nucleotide sequence of the Leptospira interrogans serovar Lai str. 56601 , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 61 nt. 2) Cytosine(C) in The sequence= 39 nt. 3) Guanine(G) in The sequence= 45 nt. 4) Thiamine(T) in The sequence= 36 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 181 nt. 8) CG percentage of The sequence= 46.41% 9) *Melting temperature of The DNA based on the Wallace formula= 80.21oC 10) The entered DNA sequence(5-3) is-181 nt.: TCTTGGAACGGAAAACTTGTTTATTCTCGTGATGAGGAAGGGAATCCGGTTCAAATCCGGAGCTGAACCCGCAGCTGTAATCGCCGAATGAGATTTCGCAATCATGCCACTGCGTTAAATACGCGGGAAGGCTGCGAAATCGGCGAAAGCCAGAAGACCTAACAAGTAAAAAAACAAACTA 11) The complementary(Com) sequence(3-5) is-181 nt.: AGAACCTTGCCTTTTGAACAAATAAGAGCACTACTCCTTCCCTTAGGCCAAGTTTAGGCCTCGACTTGGGCGTCGACATTAGCGGCTTACTCTAAAGCGTTAGTACGGTGACGCAATTTATGCGCCCTTCCGACGCTTTAGCCGCTTTCGGTCTTCTGGATTGTTCATTTTTTTGTTTGAT 12) The reverse(Rev) sequence(3-5) is-181 nt.: ATCAAACAAAAAAATGAACAATCCAGAAGACCGAAAGCGGCTAAAGCGTCGGAAGGGCGCATAAATTGCGTCACCGTACTAACGCTTTAGAGTAAGCCGCTAATGTCGACGCCCAAGTCGAGGCCTAAACTTGGCCTAAGGGAAGGAGTAGTGCTCTTATTTGTTCAAAAGGCAAGGTTCT 13) The RevCom sequence(5-3) is-181 nt.: TAGTTTGTTTTTTTACTTGTTAGGTCTTCTGGCTTTCGCCGATTTCGCAGCCTTCCCGCGTATTTAACGCAGTGGCATGATTGCGAAATCTCATTCGGCGATTACAGCTGCGGGTTCAGCTCCGGATTTGAACCGGATTCCCTTCCTCATCACGAGAATAAACAAGTTTTCCGTTCCAAGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-101 nt.: TCTTGGAACGGAAAACTTGTTTATTCTCGTGATGAGGAAGGGAATCCGGTTCAAATCCGGAGCTGAACCCGCAGCTGTAATCGCCGAATGAGATTTCGCAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-101 nt.: TAGTTTGTTTTTTTACTTGTTAGGTCTTCTGGCTTTCGCCGATTTCGCAGCCTTCCCGCGTATTTAACGCAGTGGCATGATTGCGAAATCTCATTCGGCGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Leptospira interrogans serovar Lai str. 56601 , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Leptospira interrogans serovar Lai str. 56601 , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -55.90 kcal/mol. The frequency of the MFE structure in the ensemble is 1.74 %. The ensemble diversity is 31.21. The centroid secondary structure in dot-bracket notation with a minimum free energy of -47.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Leptospira interrogans serovar Lai str. 56601 , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Leptospira interrogans serovar Lai str. 56601 , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

Below are shown the general motif sequence of the Cobalamin riboswitches and shorter motifs based on the general one: 1) N{0,18}GGTYYYN{0,12}RRRYN+AAN{0,2}GGGAAN{0,2}YGGTGN?RAN{0,2}CCRN{0,2}RCN?GYN?CCCGCN?ACTGYRARYGRN?RRN{0,14}GCCACTGRN{0,10}YYGGGAAGGYN{0,10}RN{0,5}YCRYRAGYCAGGAGACCYGCCN{0,18} 2) YCRYRAGYCAGGAGACCYGCC Motifs identified amongst the Cobalamin riboswitches based on the sequences alignment: 1) CNKNHS Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

LM530002

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Listeria monocytogenes EGD-e

Length of Switch in nucleotides

191

Sequence

TTAAATAGGTCTTATGTTGGTGGAATGTATGTACATTTCTGAAAGAGGAATTCGGTGCGATGCCGAAACTGCCCCCGCAACTGTAAGGTGGACAAGAATCGAGATAACCACTGTACGTTTTTAGCGTATGGGAAGGTTCGATTGTTGGATGAAGCCAAGTCAGGATACTCGCCAAATAAGACGGAAGCAAC

Above is displayed the nucleotide sequence of the Listeria monocytogenes EGD-e, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 58 nt. 2) Cytosine(C) in The sequence= 33 nt. 3) Guanine(G) in The sequence= 52 nt. 4) Thiamine(T) in The sequence= 48 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 191 nt. 8) CG percentage of The sequence= 44.50% 9) *Melting temperature of The DNA based on the Wallace formula= 79.63oC 10) The entered DNA sequence(5-3) is-191 nt.: TTAAATAGGTCTTATGTTGGTGGAATGTATGTACATTTCTGAAAGAGGAATTCGGTGCGATGCCGAAACTGCCCCCGCAACTGTAAGGTGGACAAGAATCGAGATAACCACTGTACGTTTTTAGCGTATGGGAAGGTTCGATTGTTGGATGAAGCCAAGTCAGGATACTCGCCAAATAAGACGGAAGCAAC 11) The complementary(Com) sequence(3-5) is-191 nt.: AATTTATCCAGAATACAACCACCTTACATACATGTAAAGACTTTCTCCTTAAGCCACGCTACGGCTTTGACGGGGGCGTTGACATTCCACCTGTTCTTAGCTCTATTGGTGACATGCAAAAATCGCATACCCTTCCAAGCTAACAACCTACTTCGGTTCAGTCCTATGAGCGGTTTATTCTGCCTTCGTTG 12) The reverse(Rev) sequence(3-5) is-191 nt.: CAACGAAGGCAGAATAAACCGCTCATAGGACTGAACCGAAGTAGGTTGTTAGCTTGGAAGGGTATGCGATTTTTGCATGTCACCAATAGAGCTAAGAACAGGTGGAATGTCAACGCCCCCGTCAAAGCCGTAGCGTGGCTTAAGGAGAAAGTCTTTACATGTATGTAAGGTGGTTGTATTCTGGATAAATT 13) The RevCom sequence(5-3) is-191 nt.: GTTGCTTCCGTCTTATTTGGCGAGTATCCTGACTTGGCTTCATCCAACAATCGAACCTTCCCATACGCTAAAAACGTACAGTGGTTATCTCGATTCTTGTCCACCTTACAGTTGCGGGGGCAGTTTCGGCATCGCACCGAATTCCTCTTTCAGAAATGTACATACATTCCACCAACATAAGACCTATTTAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-106 nt.: TTAAATAGGTCTTATGTTGGTGGAATGTATGTACATTTCTGAAAGAGGAATTCGGTGCGATGCCGAAACTGCCCCCGCAACTGTAAGGTGGACAAGAATCGAGATA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-106 nt.: GTTGCTTCCGTCTTATTTGGCGAGTATCCTGACTTGGCTTCATCCAACAATCGAACCTTCCCATACGCTAAAAACGTACAGTGGTTATCTCGATTCTTGTCCACCT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes EGD-e, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes EGD-e, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -51.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -55.27 kcal/mol. The frequency of the MFE structure in the ensemble is 0.26 %. The ensemble diversity is 29.46. The centroid secondary structure in dot-bracket notation with a minimum free energy of -41.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes EGD-e, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes EGD-e, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

MLT21331

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Mycobacterium leprae TN

Length of Switch in nucleotides

181

Sequence

GTTAGCAGGACGCGATGACGCGAGTTTCCTGGCTCTCGGATCACCGCTTGCCTCGCCTTCCAGCCAATGGCCGTGGCCTACGAGGGTCGCTCCCCGATTACAGTGGCGGGACCGCGCCGGCTTTGCACCGACTTCCTGCATCGTCATCGCCTTTACAGATACACAGTGTCGCATATAGTAC

Above is displayed the nucleotide sequence of the Mycobacterium leprae TN, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 31 nt. 2) Cytosine(C) in The sequence= 60 nt. 3) Guanine(G) in The sequence= 49 nt. 4) Thiamine(T) in The sequence= 41 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 181 nt. 8) CG percentage of The sequence= 60.22% 9) *Melting temperature of The DNA based on the Wallace formula= 85.88oC 10) The entered DNA sequence(5-3) is-181 nt.: GTTAGCAGGACGCGATGACGCGAGTTTCCTGGCTCTCGGATCACCGCTTGCCTCGCCTTCCAGCCAATGGCCGTGGCCTACGAGGGTCGCTCCCCGATTACAGTGGCGGGACCGCGCCGGCTTTGCACCGACTTCCTGCATCGTCATCGCCTTTACAGATACACAGTGTCGCATATAGTAC 11) The complementary(Com) sequence(3-5) is-181 nt.: CAATCGTCCTGCGCTACTGCGCTCAAAGGACCGAGAGCCTAGTGGCGAACGGAGCGGAAGGTCGGTTACCGGCACCGGATGCTCCCAGCGAGGGGCTAATGTCACCGCCCTGGCGCGGCCGAAACGTGGCTGAAGGACGTAGCAGTAGCGGAAATGTCTATGTGTCACAGCGTATATCATG 12) The reverse(Rev) sequence(3-5) is-181 nt.: CATGATATACGCTGTGACACATAGACATTTCCGCTACTGCTACGTCCTTCAGCCACGTTTCGGCCGCGCCAGGGCGGTGACATTAGCCCCTCGCTGGGAGCATCCGGTGCCGGTAACCGACCTTCCGCTCCGTTCGCCACTAGGCTCTCGGTCCTTTGAGCGCAGTAGCGCAGGACGATTG 13) The RevCom sequence(5-3) is-181 nt.: GTACTATATGCGACACTGTGTATCTGTAAAGGCGATGACGATGCAGGAAGTCGGTGCAAAGCCGGCGCGGTCCCGCCACTGTAATCGGGGAGCGACCCTCGTAGGCCACGGCCATTGGCTGGAAGGCGAGGCAAGCGGTGATCCGAGAGCCAGGAAACTCGCGTCATCGCGTCCTGCTAAC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-101 nt.: GTTAGCAGGACGCGATGACGCGAGTTTCCTGGCTCTCGGATCACCGCTTGCCTCGCCTTCCAGCCAATGGCCGTGGCCTACGAGGGTCGCTCCCCGATTAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-101 nt.: GTACTATATGCGACACTGTGTATCTGTAAAGGCGATGACGATGCAGGAAGTCGGTGCAAAGCCGGCGCGGTCCCGCCACTGTAATCGGGGAGCGACCCTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Mycobacterium leprae TN, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Mycobacterium leprae TN, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -57.14 kcal/mol. The frequency of the MFE structure in the ensemble is 0.85 %. The ensemble diversity is 29.99. The centroid secondary structure in dot-bracket notation with a minimum free energy of -52.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Mycobacterium leprae TN, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Mycobacterium leprae TN, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

MTH224345

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Mycobacterium tuberculosis H37Rv

Length of Switch in nucleotides

219

Sequence

GGCGCGTCCGGCACGGCTGGCAGGTCTTCGGACTCGCAGGCTCGCACCCGGTGGGTGCTCCTACTGGCCGTCGCTTCCCAGTCGTTGAGACCAGTGCTTGTCTACTTCCAAGACGGCGGTCGTTCCTGCATACCGCTGCGGGACAGTCCCGGATTCTCACCAGGTTCCCTCTCGCGAAGCATCGTTGCCCCGCTCGATGCCGACGCCCTTTCGGACGCC

Above is displayed the nucleotide sequence of the Mycobacterium tuberculosis H37Rv, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 27 nt. 2) Cytosine(C) in The sequence= 80 nt. 3) Guanine(G) in The sequence= 65 nt. 4) Thiamine(T) in The sequence= 47 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 219 nt. 8) CG percentage of The sequence= 66.21% 9) *Melting temperature of The DNA based on the Wallace formula= 88.98oC 10) The entered DNA sequence(5-3) is-219 nt.: GGCGCGTCCGGCACGGCTGGCAGGTCTTCGGACTCGCAGGCTCGCACCCGGTGGGTGCTCCTACTGGCCGTCGCTTCCCAGTCGTTGAGACCAGTGCTTGTCTACTTCCAAGACGGCGGTCGTTCCTGCATACCGCTGCGGGACAGTCCCGGATTCTCACCAGGTTCCCTCTCGCGAAGCATCGTTGCCCCGCTCGATGCCGACGCCCTTTCGGACGCC 11) The complementary(Com) sequence(3-5) is-219 nt.: CCGCGCAGGCCGTGCCGACCGTCCAGAAGCCTGAGCGTCCGAGCGTGGGCCACCCACGAGGATGACCGGCAGCGAAGGGTCAGCAACTCTGGTCACGAACAGATGAAGGTTCTGCCGCCAGCAAGGACGTATGGCGACGCCCTGTCAGGGCCTAAGAGTGGTCCAAGGGAGAGCGCTTCGTAGCAACGGGGCGAGCTACGGCTGCGGGAAAGCCTGCGG 12) The reverse(Rev) sequence(3-5) is-219 nt.: CCGCAGGCTTTCCCGCAGCCGTAGCTCGCCCCGTTGCTACGAAGCGCTCTCCCTTGGACCACTCTTAGGCCCTGACAGGGCGTCGCCATACGTCCTTGCTGGCGGCAGAACCTTCATCTGTTCGTGACCAGAGTTGCTGACCCTTCGCTGCCGGTCATCCTCGTGGGTGGCCCACGCTCGGACGCTCAGGCTTCTGGACGGTCGGCACGGCCTGCGCGG 13) The RevCom sequence(5-3) is-219 nt.: GGCGTCCGAAAGGGCGTCGGCATCGAGCGGGGCAACGATGCTTCGCGAGAGGGAACCTGGTGAGAATCCGGGACTGTCCCGCAGCGGTATGCAGGAACGACCGCCGTCTTGGAAGTAGACAAGCACTGGTCTCAACGACTGGGAAGCGACGGCCAGTAGGAGCACCCACCGGGTGCGAGCCTGCGAGTCCGAAGACCTGCCAGCCGTGCCGGACGCGCC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-120 nt.: GGCGCGTCCGGCACGGCTGGCAGGTCTTCGGACTCGCAGGCTCGCACCCGGTGGGTGCTCCTACTGGCCGTCGCTTCCCAGTCGTTGAGACCAGTGCTTGTCTACTTCCAAGACGGCGGT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-120 nt.: GGCGTCCGAAAGGGCGTCGGCATCGAGCGGGGCAACGATGCTTCGCGAGAGGGAACCTGGTGAGAATCCGGGACTGTCCCGCAGCGGTATGCAGGAACGACCGCCGTCTTGGAAGTAGAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Mycobacterium tuberculosis H37Rv, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Mycobacterium tuberculosis H37Rv, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -84.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -88.05 kcal/mol. The frequency of the MFE structure in the ensemble is 0.27 %. The ensemble diversity is 69.14. The centroid secondary structure in dot-bracket notation with a minimum free energy of -49.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Mycobacterium tuberculosis H37Rv, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Mycobacterium tuberculosis H37Rv, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

PR431009

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Pseudomonas resinovorans NBRC 106553

Length of Switch in nucleotides

196

Sequence

TGTCTGGAATATCGTCGAGGCAGGTCTCCTGGCTCACAGCCTGGCGCGTTGCGCCGTCTCTCCGCCTTCCCGCCCGAGGGGCAGTGGCTGTGGATAAGACATCAGCTGTTCACAGTTGCGGGGGCAGCCGTGGTTTGGACCACGTTCCCTCTTAGCTCCGGCGCCTGGCCGGAGAACCTCGAAAGGGCGAAGGCTA

Above is displayed the nucleotide sequence of the Pseudomonas resinovorans NBRC 106553 , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 30 nt. 2) Cytosine(C) in The sequence= 60 nt. 3) Guanine(G) in The sequence= 65 nt. 4) Thiamine(T) in The sequence= 41 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 196 nt. 8) CG percentage of The sequence= 63.78% 9) *Melting temperature of The DNA based on the Wallace formula= 87.62oC 10) The entered DNA sequence(5-3) is-196 nt.: TGTCTGGAATATCGTCGAGGCAGGTCTCCTGGCTCACAGCCTGGCGCGTTGCGCCGTCTCTCCGCCTTCCCGCCCGAGGGGCAGTGGCTGTGGATAAGACATCAGCTGTTCACAGTTGCGGGGGCAGCCGTGGTTTGGACCACGTTCCCTCTTAGCTCCGGCGCCTGGCCGGAGAACCTCGAAAGGGCGAAGGCTA 11) The complementary(Com) sequence(3-5) is-196 nt.: ACAGACCTTATAGCAGCTCCGTCCAGAGGACCGAGTGTCGGACCGCGCAACGCGGCAGAGAGGCGGAAGGGCGGGCTCCCCGTCACCGACACCTATTCTGTAGTCGACAAGTGTCAACGCCCCCGTCGGCACCAAACCTGGTGCAAGGGAGAATCGAGGCCGCGGACCGGCCTCTTGGAGCTTTCCCGCTTCCGAT 12) The reverse(Rev) sequence(3-5) is-196 nt.: ATCGGAAGCGGGAAAGCTCCAAGAGGCCGGTCCGCGGCCTCGATTCTCCCTTGCACCAGGTTTGGTGCCGACGGGGGCGTTGACACTTGTCGACTACAGAATAGGTGTCGGTGACGGGGAGCCCGCCCTTCCGCCTCTCTGCCGCGTTGCGCGGTCCGACACTCGGTCCTCTGGACGGAGCTGCTATAAGGTCTGT 13) The RevCom sequence(5-3) is-196 nt.: TAGCCTTCGCCCTTTCGAGGTTCTCCGGCCAGGCGCCGGAGCTAAGAGGGAACGTGGTCCAAACCACGGCTGCCCCCGCAACTGTGAACAGCTGATGTCTTATCCACAGCCACTGCCCCTCGGGCGGGAAGGCGGAGAGACGGCGCAACGCGCCAGGCTGTGAGCCAGGAGACCTGCCTCGACGATATTCCAGACA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-108 nt.: TGTCTGGAATATCGTCGAGGCAGGTCTCCTGGCTCACAGCCTGGCGCGTTGCGCCGTCTCTCCGCCTTCCCGCCCGAGGGGCAGTGGCTGTGGATAAGACATCAGCTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-108 nt.: TAGCCTTCGCCCTTTCGAGGTTCTCCGGCCAGGCGCCGGAGCTAAGAGGGAACGTGGTCCAAACCACGGCTGCCCCCGCAACTGTGAACAGCTGATGTCTTATCCACA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Pseudomonas resinovorans NBRC 106553 , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Pseudomonas resinovorans NBRC 106553 , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -88.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -91.06 kcal/mol. The frequency of the MFE structure in the ensemble is 0.82 %. The ensemble diversity is 23.63. The centroid secondary structure in dot-bracket notation with a minimum free energy of -87.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Pseudomonas resinovorans NBRC 106553 , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Pseudomonas resinovorans NBRC 106553 , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

SE320011

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Salmonella enterica subsp. arizonae serovar 62

Length of Switch in nucleotides

176

Sequence

CCATAACGTAAACCAACAGGTTTACCACATTTGTGGTAGGGAAGGGGGTTAAAATCCCCCGCAGCCCCCGCTGCTGTGATGCTGACGACCCCGTAAAAACCACTGATCGCAAGATTGGGAAGGACGGGCGAGGATGACGCTAAGCCAGAAGACCTGCCTGTCGGTGATAACCAACA

Above is displayed the nucleotide sequence of the Salmonella enterica subsp. arizonae serovar 62, Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 51 nt. 2) Cytosine(C) in The sequence= 47 nt. 3) Guanine(G) in The sequence= 48 nt. 4) Thiamine(T) in The sequence= 30 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 176 nt. 8) CG percentage of The sequence= 53.98% 9) *Melting temperature of The DNA based on the Wallace formula= 83.21oC 10) The entered DNA sequence(5-3) is-176 nt.: CCATAACGTAAACCAACAGGTTTACCACATTTGTGGTAGGGAAGGGGGTTAAAATCCCCCGCAGCCCCCGCTGCTGTGATGCTGACGACCCCGTAAAAACCACTGATCGCAAGATTGGGAAGGACGGGCGAGGATGACGCTAAGCCAGAAGACCTGCCTGTCGGTGATAACCAACA 11) The complementary(Com) sequence(3-5) is-176 nt.: GGTATTGCATTTGGTTGTCCAAATGGTGTAAACACCATCCCTTCCCCCAATTTTAGGGGGCGTCGGGGGCGACGACACTACGACTGCTGGGGCATTTTTGGTGACTAGCGTTCTAACCCTTCCTGCCCGCTCCTACTGCGATTCGGTCTTCTGGACGGACAGCCACTATTGGTTGT 12) The reverse(Rev) sequence(3-5) is-176 nt.: ACAACCAATAGTGGCTGTCCGTCCAGAAGACCGAATCGCAGTAGGAGCGGGCAGGAAGGGTTAGAACGCTAGTCACCAAAAATGCCCCAGCAGTCGTAGTGTCGTCGCCCCCGACGCCCCCTAAAATTGGGGGAAGGGATGGTGTTTACACCATTTGGACAACCAAATGCAATACC 13) The RevCom sequence(5-3) is-176 nt.: TGTTGGTTATCACCGACAGGCAGGTCTTCTGGCTTAGCGTCATCCTCGCCCGTCCTTCCCAATCTTGCGATCAGTGGTTTTTACGGGGTCGTCAGCATCACAGCAGCGGGGGCTGCGGGGGATTTTAACCCCCTTCCCTACCACAAATGTGGTAAACCTGTTGGTTTACGTTATGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-98 nt.: CCATAACGTAAACCAACAGGTTTACCACATTTGTGGTAGGGAAGGGGGTTAAAATCCCCCGCAGCCCCCGCTGCTGTGATGCTGACGACCCCGTAAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-98 nt.: TGTTGGTTATCACCGACAGGCAGGTCTTCTGGCTTAGCGTCATCCTCGCCCGTCCTTCCCAATCTTGCGATCAGTGGTTTTTACGGGGTCGTCAGCAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella enterica subsp. arizonae serovar 62, Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella enterica subsp. arizonae serovar 62, Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -55.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -59.33 kcal/mol. The frequency of the MFE structure in the ensemble is 0.38 %. The ensemble diversity is 37.62. The centroid secondary structure in dot-bracket notation with a minimum free energy of -42.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella enterica subsp. arizonae serovar 62, Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella enterica subsp. arizonae serovar 62, Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

YP90002

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Yersinia pestis CO92

Length of Switch in nucleotides

263

Sequence

ATATTGCGACGTAATACCGGCAGGTCTTCGGGCTTAGGATCTCTGGTATCAGGCCATGGTTATGACAGTAAAAATACTGTGATAAATAAATGGCGCGAAATAGAGCAGGCGATGACTTCCCATCCTTGCGGACAGTGTCTGTTAGAAACCTATCGCCGTGACTTCCCCTTACCGCTGCGCGTCAGCTCCGGATTTACACCGGATTCCCTTTTAACTCTTAGGTGTTTAAATAACAGCATGAGGCCGGACCACAATGCTACGAT

Above is displayed the nucleotide sequence of the Yersinia pestis CO92 , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 68 nt. 2) Cytosine(C) in The sequence= 64 nt. 3) Guanine(G) in The sequence= 62 nt. 4) Thiamine(T) in The sequence= 69 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 263 nt. 8) CG percentage of The sequence= 47.91% 9) *Melting temperature of The DNA based on the Wallace formula= 81.99oC 10) The entered DNA sequence(5-3) is-263 nt.: ATATTGCGACGTAATACCGGCAGGTCTTCGGGCTTAGGATCTCTGGTATCAGGCCATGGTTATGACAGTAAAAATACTGTGATAAATAAATGGCGCGAAATAGAGCAGGCGATGACTTCCCATCCTTGCGGACAGTGTCTGTTAGAAACCTATCGCCGTGACTTCCCCTTACCGCTGCGCGTCAGCTCCGGATTTACACCGGATTCCCTTTTAACTCTTAGGTGTTTAAATAACAGCATGAGGCCGGACCACAATGCTACGAT 11) The complementary(Com) sequence(3-5) is-263 nt.: TATAACGCTGCATTATGGCCGTCCAGAAGCCCGAATCCTAGAGACCATAGTCCGGTACCAATACTGTCATTTTTATGACACTATTTATTTACCGCGCTTTATCTCGTCCGCTACTGAAGGGTAGGAACGCCTGTCACAGACAATCTTTGGATAGCGGCACTGAAGGGGAATGGCGACGCGCAGTCGAGGCCTAAATGTGGCCTAAGGGAAAATTGAGAATCCACAAATTTATTGTCGTACTCCGGCCTGGTGTTACGATGCTA 12) The reverse(Rev) sequence(3-5) is-263 nt.: TAGCATCGTAACACCAGGCCGGAGTACGACAATAAATTTGTGGATTCTCAATTTTCCCTTAGGCCACATTTAGGCCTCGACTGCGCGTCGCCATTCCCCTTCAGTGCCGCTATCCAAAGATTGTCTGTGACAGGCGTTCCTACCCTTCAGTAGCGGACGAGATAAAGCGCGGTAAATAAATAGTGTCATAAAAATGACAGTATTGGTACCGGACTATGGTCTCTAGGATTCGGGCTTCTGGACGGCCATAATGCAGCGTTATA 13) The RevCom sequence(5-3) is-263 nt.: ATCGTAGCATTGTGGTCCGGCCTCATGCTGTTATTTAAACACCTAAGAGTTAAAAGGGAATCCGGTGTAAATCCGGAGCTGACGCGCAGCGGTAAGGGGAAGTCACGGCGATAGGTTTCTAACAGACACTGTCCGCAAGGATGGGAAGTCATCGCCTGCTCTATTTCGCGCCATTTATTTATCACAGTATTTTTACTGTCATAACCATGGCCTGATACCAGAGATCCTAAGCCCGAAGACCTGCCGGTATTACGTCGCAATAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-142 nt.: ATATTGCGACGTAATACCGGCAGGTCTTCGGGCTTAGGATCTCTGGTATCAGGCCATGGTTATGACAGTAAAAATACTGTGATAAATAAATGGCGCGAAATAGAGCAGGCGATGACTTCCCATCCTTGCGGACAGTGTCTGT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-142 nt.: ATCGTAGCATTGTGGTCCGGCCTCATGCTGTTATTTAAACACCTAAGAGTTAAAAGGGAATCCGGTGTAAATCCGGAGCTGACGCGCAGCGGTAAGGGGAAGTCACGGCGATAGGTTTCTAACAGACACTGTCCGCAAGGAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Yersinia pestis CO92 , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Yersinia pestis CO92 , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -74.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -77.81 kcal/mol. The frequency of the MFE structure in the ensemble is 0.33 %. The ensemble diversity is 67.68. The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Yersinia pestis CO92 , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Yersinia pestis CO92 , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

VCB85432

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RiboSwitch type

Cobalamin type switch

Bacteria strain target

Vibrio cholerae O1 biovar eltor str. N16961

Length of Switch in nucleotides

204

Sequence

TACTATCAGCGCCAAGCTGGTGCTATTTAGATGCCTGGATGGCTAAAAATGGCTGAAAAGGGAATCCGGTGTAACTCCGGAACTGACGCGCAGCGGTAAGAGAGAACGAACGCTCAAACG ACACTGCTTTTCGAGTGGGAAGTCGAGCCAGTAGGCCAACAGTGCTCTCAAGTCCGAAGACCTGCCAGCAACTGAGTTATGCAG

Above is displayed the nucleotide sequence of the Vibrio cholerae O1 biovar eltor str. N16961 , Cobalamin type switch.

Sequence information and analysis

1) Adenine(A) in The sequence= 59 nt. 2) Cytosine(C) in The sequence= 48 nt. 3) Guanine(G) in The sequence= 58 nt. 4) Thiamine(T) in The sequence= 39 nt. 5) *Mistaken symbols in The sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in The sequence= 7) All nucleotides in The sequence= 204 nt. 8) CG percentage of The sequence= 51.96% 9) *Melting temperature of The DNA based on the Wallace formula= 82.91oC 10) The entered DNA sequence(5-3) is-204 nt.: TACTATCAGCGCCAAGCTGGTGCTATTTAGATGCCTGGATGGCTAAAAATGGCTGAAAAGGGAATCCGGTGTAACTCCGGAACTGACGCGCAGCGGTAAGAGAGAACGAACGCTCAAACGACACTGCTTTTCGAGTGGGAAGTCGAGCCAGTAGGCCAACAGTGCTCTCAAGTCCGAAGACCTGCCAGCAACTGAGTTATGCAG 11) The complementary(Com) sequence(3-5) is-204 nt.: ATGATAGTCGCGGTTCGACCACGATAAATCTACGGACCTACCGATTTTTACCGACTTTTCCCTTAGGCCACATTGAGGCCTTGACTGCGCGTCGCCATTCTCTCTTGCTTGCGAGTTTGCTGTGACGAAAAGCTCACCCTTCAGCTCGGTCATCCGGTTGTCACGAGAGTTCAGGCTTCTGGACGGTCGTTGACTCAATACGTC 12) The reverse(Rev) sequence(3-5) is-204 nt.: GACGTATTGAGTCAACGACCGTCCAGAAGCCTGAACTCTCGTGACAACCGGATGACCGAGCTGAAGGGTGAGCTTTTCGTCACAGCAAACTCGCAAGCAAGAGAGAATGGCGACGCGCAGTCAAGGCCTCAATGTGGCCTAAGGGAAAAGTCGGTAAAAATCGGTAGGTCCGTAGATTTATCGTGGTCGAACCGCGACTATCAT 13) The RevCom sequence(5-3) is-204 nt.: CTGCATAACTCAGTTGCTGGCAGGTCTTCGGACTTGAGAGCACTGTTGGCCTACTGGCTCGACTTCCCACTCGAAAAGCAGTGTCGTTTGAGCGTTCGTTCTCTCTTACCGCTGCGCGTCAGTTCCGGAGTTACACCGGATTCCCTTTTCAGCCATTTTTAGCCATCCAGGCATCTAAATAGCACCAGCTTGGCGCTGATAGTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-112 nt.: TACTATCAGCGCCAAGCTGGTGCTATTTAGATGCCTGGATGGCTAAAAATGGCTGAAAAGGGAATCCGGTGTAACTCCGGAACTGACGCGCAGCGGTAAGAGAGAACGAACG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-112 nt.: CTGCATAACTCAGTTGCTGGCAGGTCTTCGGACTTGAGAGCACTGTTGGCCTACTGGCTCGACTTCCCACTCGAAAAGCAGTGTCGTTTGAGCGTTCGTTCTCTCTTACCGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Vibrio cholerae O1 biovar eltor str. N16961 , Cobalamin type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Vibrio cholerae O1 biovar eltor str. N16961 , Cobalamin type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -58.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -61.03 kcal/mol. The frequency of the MFE structure in the ensemble is 0.87 %. The ensemble diversity is 33.35. The centroid secondary structure in dot-bracket notation with a minimum free energy of -45.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Vibrio cholerae O1 biovar eltor str. N16961 , Cobalamin type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Vibrio cholerae O1 biovar eltor str. N16961 , Cobalamin type switch.

Multiple alignment of the Cobalamin type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cobalamin type switches involved in.

Multi_resistance strains for the Cobalamin type switches

RiboSwitch_ID:

BA386482

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RiboSwitch type

Lysine type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

182

Sequence

CCTCTCGATAGCTCTCCACAAACGAAACGTTTGTGACAGTTCTGCACTTATTAAATGCAGACCCAGCAAGTGTGCATGGTGGACACAACTTACTTCGGCAATCATTCCTTTCTCATTCCTTCATCAATGCCACTACATCTCCAGAAATGATACTCTTAATGACTGCAACCTCTACCTCACCG

Above is displayed the nucleotide sequence of the Bacillus anthracis, Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 50 nt. 2) Cytosine(C) in the sequence= 55 nt. 3) Guanine(G) in the sequence= 26 nt. 4) Thiamine(T) in the sequence= 51 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 182 nt. 8) CG percentage of the sequence= 44.51% 9) *Melting temperature of the DNA based on the Wallace formula= 79.45oC 10) The entered DNA sequence(5-3) is-182 nt.: CCTCTCGATAGCTCTCCACAAACGAAACGTTTGTGACAGTTCTGCACTTATTAAATGCAGACCCAGCAAGTGTGCATGGTGGACACAACTTACTTCGGCAATCATTCCTTTCTCATTCCTTCATCAATGCCACTACATCTCCAGAAATGATACTCTTAATGACTGCAACCTCTACCTCACCG 11) The complementary(Com) sequence(3-5) is-182 nt.: GGAGAGCTATCGAGAGGTGTTTGCTTTGCAAACACTGTCAAGACGTGAATAATTTACGTCTGGGTCGTTCACACGTACCACCTGTGTTGAATGAAGCCGTTAGTAAGGAAAGAGTAAGGAAGTAGTTACGGTGATGTAGAGGTCTTTACTATGAGAATTACTGACGTTGGAGATGGAGTGGC 12) The reverse(Rev) sequence(3-5) is-182 nt.: GCCACTCCATCTCCAACGTCAGTAATTCTCATAGTAAAGACCTCTACATCACCGTAACTACTTCCTTACTCTTTCCTTACTAACGGCTTCATTCAACACAGGTGGTACGTGTGAACGACCCAGACGTAAATTATTCACGTCTTGACAGTGTTTGCAAAGCAAACACCTCTCGATAGCTCTCC 13) The RevCom sequence(5-3) is-182 nt.: CGGTGAGGTAGAGGTTGCAGTCATTAAGAGTATCATTTCTGGAGATGTAGTGGCATTGATGAAGGAATGAGAAAGGAATGATTGCCGAAGTAAGTTGTGTCCACCATGCACACTTGCTGGGTCTGCATTTAATAAGTGCAGAACTGTCACAAACGTTTCGTTTGTGGAGAGCTATCGAGAGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-101 nt.: CCTCTCGATAGCTCTCCACAAACGAAACGTTTGTGACAGTTCTGCACTTATTAAATGCAGACCCAGCAAGTGTGCATGGTGGACACAACTTACTTCGGCAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-101 nt.: CGGTGAGGTAGAGGTTGCAGTCATTAAGAGTATCATTTCTGGAGATGTAGTGGCATTGATGAAGGAATGAGAAAGGAATGATTGCCGAAGTAAGTTGTGTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis, Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis, Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -57.84 kcal/mol. The frequency of the MFE structure in the ensemble is 0.72 %. The ensemble diversity is 31.38. The centroid secondary structure in dot-bracket notation with a minimum free energy of -50.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis, Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis, Lysine type switch.

Multiple alignment of the Lysine type switches

Below is presented the sequences alignment of all the Lysine type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Lysine type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Lysin riboswitches and shorter motifs based on the general one: 1) N?RN{0,5}RN?AGAGGYGCRN{0,4}YN?AN{0,2}AGTAN{0,5}YN{0,6}RN?RN{0,2}RN{0,4}YRRYGAN{0,2}RN{0,4}YGAARGGN?RN{0,2}RN?YGCCGAARYN?RN{0,3}RRN{0,6}YN{0,3}YYGYTGGN{0,3}YRYRN{0,3}AAN{0,2}RN{0,2}RYN?RN?AYTGTCAYN?RN{0,8}YYRTGGAGN?GCTAYYN{0,6} Motifs identified amongst the Lysin riboswitches based on the sequences alignment: 1) AHBTCGGCRNT 2) RHBYHBDYRNY Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

The table displays known human pathogenic bacteria bearing the Lysine type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BC1425432

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RiboSwitch type

Lysine type switch

Bacteria strain target

Bacillus cereus

Length of Switch in nucleotides

182

Sequence

CGGTGAGGTAGAGGTTGCAGTCATTAAGAGTATCATTTCAGGAGATGTAGTGGCATTGATGAAGAAATGAGAAAGGAATGATTGCCGAAGTAAGTCGTGTCCACCATGCACACTTGCTGGGTCTGCATTTAATAAGTGCAGAACTGTCACAAACGTTTCGTTTGTGGAGAGCTATCGAGAGG

Above is displayed the nucleotide sequence of the Bacillus cereus, Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 53 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 54 nt. 4) Thiamine(T) in the sequence= 48 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 182 nt. 8) CG percentage of the sequence= 44.51% 9) *Melting temperature of the DNA based on the Wallace formula= 79.45oC 10) The entered DNA sequence(5-3) is-182 nt.: CGGTGAGGTAGAGGTTGCAGTCATTAAGAGTATCATTTCAGGAGATGTAGTGGCATTGATGAAGAAATGAGAAAGGAATGATTGCCGAAGTAAGTCGTGTCCACCATGCACACTTGCTGGGTCTGCATTTAATAAGTGCAGAACTGTCACAAACGTTTCGTTTGTGGAGAGCTATCGAGAGG 11) The complementary(Com) sequence(3-5) is-182 nt.: GCCACTCCATCTCCAACGTCAGTAATTCTCATAGTAAAGTCCTCTACATCACCGTAACTACTTCTTTACTCTTTCCTTACTAACGGCTTCATTCAGCACAGGTGGTACGTGTGAACGACCCAGACGTAAATTATTCACGTCTTGACAGTGTTTGCAAAGCAAACACCTCTCGATAGCTCTCC 12) The reverse(Rev) sequence(3-5) is-182 nt.: GGAGAGCTATCGAGAGGTGTTTGCTTTGCAAACACTGTCAAGACGTGAATAATTTACGTCTGGGTCGTTCACACGTACCACCTGTGCTGAATGAAGCCGTTAGTAAGGAAAGAGTAAAGAAGTAGTTACGGTGATGTAGAGGACTTTACTATGAGAATTACTGACGTTGGAGATGGAGTGGC 13) The RevCom sequence(5-3) is-182 nt.: CCTCTCGATAGCTCTCCACAAACGAAACGTTTGTGACAGTTCTGCACTTATTAAATGCAGACCCAGCAAGTGTGCATGGTGGACACGACTTACTTCGGCAATCATTCCTTTCTCATTTCTTCATCAATGCCACTACATCTCCTGAAATGATACTCTTAATGACTGCAACCTCTACCTCACCG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-101 nt.: CGGTGAGGTAGAGGTTGCAGTCATTAAGAGTATCATTTCAGGAGATGTAGTGGCATTGATGAAGAAATGAGAAAGGAATGATTGCCGAAGTAAGTCGTGTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-101 nt.: CCTCTCGATAGCTCTCCACAAACGAAACGTTTGTGACAGTTCTGCACTTATTAAATGCAGACCCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus cereus, Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus cereus, Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -56.99 kcal/mol. The frequency of the MFE structure in the ensemble is 1.50 %. The ensemble diversity is 15.53. The centroid secondary structure in dot-bracket notation with a minimum free energy of -53.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus cereus, Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus cereus, Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

BS9357005

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RiboSwitch type

Lysine type switch

Bacteria strain target

Bacillus subtilis

Length of Switch in nucleotides

180

Sequence

CAACGAGATAGCCCTCCAAGAAAATGATTTCTTGACAGCCTTACATTTATTCAATGCACGGCCAGCAAATAATACCGATGGGGTTTTATTTGCTTCGGCGACGCTCCCCTTTCAGCCTTTTTCACAGAATCCATCTTTCTCCAAAGGCATACTCTTGAAGTTCGCACCTCTATCTTCACC

Above is displayed the nucleotide sequence of the Bacillus subtilis , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 46 nt. 2) Cytosine(C) in the sequence= 52 nt. 3) Guanine(G) in the sequence= 28 nt. 4) Thiamine(T) in the sequence= 54 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 180 nt. 8) CG percentage of the sequence= 44.44% 9) *Melting temperature of the DNA based on the Wallace formula= 79.39oC 10) The entered DNA sequence(5-3) is-180 nt.: CAACGAGATAGCCCTCCAAGAAAATGATTTCTTGACAGCCTTACATTTATTCAATGCACGGCCAGCAAATAATACCGATGGGGTTTTATTTGCTTCGGCGACGCTCCCCTTTCAGCCTTTTTCACAGAATCCATCTTTCTCCAAAGGCATACTCTTGAAGTTCGCACCTCTATCTTCACC 11) The complementary(Com) sequence(3-5) is-180 nt.: GTTGCTCTATCGGGAGGTTCTTTTACTAAAGAACTGTCGGAATGTAAATAAGTTACGTGCCGGTCGTTTATTATGGCTACCCCAAAATAAACGAAGCCGCTGCGAGGGGAAAGTCGGAAAAAGTGTCTTAGGTAGAAAGAGGTTTCCGTATGAGAACTTCAAGCGTGGAGATAGAAGTGG 12) The reverse(Rev) sequence(3-5) is-180 nt.: CCACTTCTATCTCCACGCTTGAAGTTCTCATACGGAAACCTCTTTCTACCTAAGACACTTTTTCCGACTTTCCCCTCGCAGCGGCTTCGTTTATTTTGGGGTAGCCATAATAAACGACCGGCACGTAACTTATTTACATTCCGACAGTTCTTTAGTAAAAGAACCTCCCGATAGAGCAAC 13) The RevCom sequence(5-3) is-180 nt.: GGTGAAGATAGAGGTGCGAACTTCAAGAGTATGCCTTTGGAGAAAGATGGATTCTGTGAAAAAGGCTGAAAGGGGAGCGTCGCCGAAGCAAATAAAACCCCATCGGTATTATTTGCTGGCCGTGCATTGAATAAATGTAAGGCTGTCAAGAAATCATTTTCTTGGAGGGCTATCTCGTTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-100 nt.: CAACGAGATAGCCCTCCAAGAAAATGATTTCTTGACAGCCTTACATTTATTCAATGCACGGCCAGCAAATAATACCGATGGGGTTTTATTTGCTTCGGCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-100 nt.: GGTGAAGATAGAGGTGCGAACTTCAAGAGTATGCCTTTGGAGAAAGATGGATTCTGTGAAAAAGGCTGAAAGGGGAGCGTCGCCGAAGCAAATAAAACCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -41.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -44.01 kcal/mol. The frequency of the MFE structure in the ensemble is 2.77 %. The ensemble diversity is 11.61. The centroid secondary structure in dot-bracket notation with a minimum free energy of -38.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

CB4628001

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RiboSwitch type

Lysine type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

175

Sequence

TAAGTAGATAGAGGTGCGATGTTAATTAGTACTTTTACGAAGGTAAGCGCTATGAAGTAAAAGGAAAGGGAATATCGCCGAAGTACACAGCTGATGCTTTAAGGTTGTATACTGGGGTTGCATAGAATATGTGTAACACTGTCACAAATTTATTTTGTGGAGAGCTATCATTCAA

Above is displayed the nucleotide sequence of the Clostridium botulinum , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 58 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 44 nt. 4) Thiamine(T) in the sequence= 52 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 175 nt. 8) CG percentage of the sequence= 37.14% 9) *Melting temperature of the DNA based on the Wallace formula= 76.29oC 10) The entered DNA sequence(5-3) is-175 nt.: TAAGTAGATAGAGGTGCGATGTTAATTAGTACTTTTACGAAGGTAAGCGCTATGAAGTAAAAGGAAAGGGAATATCGCCGAAGTACACAGCTGATGCTTTAAGGTTGTATACTGGGGTTGCATAGAATATGTGTAACACTGTCACAAATTTATTTTGTGGAGAGCTATCATTCAA 11) The complementary(Com) sequence(3-5) is-175 nt.: ATTCATCTATCTCCACGCTACAATTAATCATGAAAATGCTTCCATTCGCGATACTTCATTTTCCTTTCCCTTATAGCGGCTTCATGTGTCGACTACGAAATTCCAACATATGACCCCAACGTATCTTATACACATTGTGACAGTGTTTAAATAAAACACCTCTCGATAGTAAGTT 12) The reverse(Rev) sequence(3-5) is-175 nt.: AACTTACTATCGAGAGGTGTTTTATTTAAACACTGTCACAATGTGTATAAGATACGTTGGGGTCATATGTTGGAATTTCGTAGTCGACACATGAAGCCGCTATAAGGGAAAGGAAAATGAAGTATCGCGAATGGAAGCATTTTCATGATTAATTGTAGCGTGGAGATAGATGAAT 13) The RevCom sequence(5-3) is-175 nt.: TTGAATGATAGCTCTCCACAAAATAAATTTGTGACAGTGTTACACATATTCTATGCAACCCCAGTATACAACCTTAAAGCATCAGCTGTGTACTTCGGCGATATTCCCTTTCCTTTTACTTCATAGCGCTTACCTTCGTAAAAGTACTAATTAACATCGCACCTCTATCTACTTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-98 nt.: TAAGTAGATAGAGGTGCGATGTTAATTAGTACTTTTACGAAGGTAAGCGCTATGAAGTAAAAGGAAAGGGAATATCGCCGAAGTACACAGCTGATGCT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-98 nt.: TTGAATGATAGCTCTCCACAAAATAAATTTGTGACAGTGTTACACATATTCTATGCAACCCCAGTATACAACCTTAAAGCATCAGCTGTGTACTTCGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -42.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -45.78 kcal/mol. The frequency of the MFE structure in the ensemble is 0.67 %. The ensemble diversity is 12.65. The centroid secondary structure in dot-bracket notation with a minimum free energy of -39.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

CD1424903

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RiboSwitch type

Lysine type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

180

Sequence

GTTTAAGATAGCTCTCCATCAAAATTCGGGATAATTTTGATGACAGTACTGTACCTATTAAATACAGTCCCAGCACTAGCTTCGGACACTAGCACTTCGGCACTTACTCCTTTTATATTGCCTCATTGGTTTCCAACCTCTTCAATATTAATCTTAGTAAATGCAACCTCTACCTCAATC

Above is displayed the nucleotide sequence of the Clostridium difficile , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 51 nt. 2) Cytosine(C) in the sequence= 46 nt. 3) Guanine(G) in the sequence= 23 nt. 4) Thiamine(T) in the sequence= 60 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 180 nt. 8) CG percentage of the sequence= 38.33% 9) *Melting temperature of the DNA based on the Wallace formula= 76.88oC 10) The entered DNA sequence(5-3) is-180 nt.: GTTTAAGATAGCTCTCCATCAAAATTCGGGATAATTTTGATGACAGTACTGTACCTATTAAATACAGTCCCAGCACTAGCTTCGGACACTAGCACTTCGGCACTTACTCCTTTTATATTGCCTCATTGGTTTCCAACCTCTTCAATATTAATCTTAGTAAATGCAACCTCTACCTCAATC 11) The complementary(Com) sequence(3-5) is-180 nt.: CAAATTCTATCGAGAGGTAGTTTTAAGCCCTATTAAAACTACTGTCATGACATGGATAATTTATGTCAGGGTCGTGATCGAAGCCTGTGATCGTGAAGCCGTGAATGAGGAAAATATAACGGAGTAACCAAAGGTTGGAGAAGTTATAATTAGAATCATTTACGTTGGAGATGGAGTTAG 12) The reverse(Rev) sequence(3-5) is-180 nt.: CTAACTCCATCTCCAACGTAAATGATTCTAATTATAACTTCTCCAACCTTTGGTTACTCCGTTATATTTTCCTCATTCACGGCTTCACGATCACAGGCTTCGATCACGACCCTGACATAAATTATCCATGTCATGACAGTAGTTTTAATAGGGCTTAAAACTACCTCTCGATAGAATTTG 13) The RevCom sequence(5-3) is-180 nt.: GATTGAGGTAGAGGTTGCATTTACTAAGATTAATATTGAAGAGGTTGGAAACCAATGAGGCAATATAAAAGGAGTAAGTGCCGAAGTGCTAGTGTCCGAAGCTAGTGCTGGGACTGTATTTAATAGGTACAGTACTGTCATCAAAATTATCCCGAATTTTGATGGAGAGCTATCTTAAAC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-100 nt.: GTTTAAGATAGCTCTCCATCAAAATTCGGGATAATTTTGATGACAGTACTGTACCTATTAAATACAGTCCCAGCACTAGCTTCGGACACTAGCACTTCGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-100 nt.: GATTGAGGTAGAGGTTGCATTTACTAAGATTAATATTGAAGAGGTTGGAAACCAATGAGGCAATATAAAAGGAGTAAGTGCCGAAGTGCTAGTGTCCGAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -29.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -32.63 kcal/mol. The frequency of the MFE structure in the ensemble is 0.74 %. The ensemble diversity is 23.32. The centroid secondary structure in dot-bracket notation with a minimum free energy of -26.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

CP3623001

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RiboSwitch type

Lysine type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

170

Sequence

TAAGATGATAGCTCTCCACATTTTGTGACAGTGTTGTATATATTCTATACAACCCCAGCATTTAGCCTTAAAGTATTAGCCAAAAACTTCGGCGATAATCCCTTTCCTAAAACTTCTACGCTACTTAACTCCATTTTAGTAATCTTGATTCTCGCGCCTCTACCTCTTTT

Above is displayed the nucleotide sequence of the Clostridium perfringens , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 46 nt. 2) Cytosine(C) in the sequence= 43 nt. 3) Guanine(G) in the sequence= 20 nt. 4) Thiamine(T) in the sequence= 61 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 170 nt. 8) CG percentage of the sequence= 37.06% 9) *Melting temperature of the DNA based on the Wallace formula= 76.14oC 10) The entered DNA sequence(5-3) is-170 nt.: TAAGATGATAGCTCTCCACATTTTGTGACAGTGTTGTATATATTCTATACAACCCCAGCATTTAGCCTTAAAGTATTAGCCAAAAACTTCGGCGATAATCCCTTTCCTAAAACTTCTACGCTACTTAACTCCATTTTAGTAATCTTGATTCTCGCGCCTCTACCTCTTTT 11) The complementary(Com) sequence(3-5) is-170 nt.: ATTCTACTATCGAGAGGTGTAAAACACTGTCACAACATATATAAGATATGTTGGGGTCGTAAATCGGAATTTCATAATCGGTTTTTGAAGCCGCTATTAGGGAAAGGATTTTGAAGATGCGATGAATTGAGGTAAAATCATTAGAACTAAGAGCGCGGAGATGGAGAAAA 12) The reverse(Rev) sequence(3-5) is-170 nt.: TTTTCTCCATCTCCGCGCTCTTAGTTCTAATGATTTTACCTCAATTCATCGCATCTTCAAAATCCTTTCCCTAATAGCGGCTTCAAAAACCGATTATGAAATTCCGATTTACGACCCCAACATATCTTATATATGTTGTGACAGTGTTTTACACCTCTCGATAGTAGAAT 13) The RevCom sequence(5-3) is-170 nt.: AAAAGAGGTAGAGGCGCGAGAATCAAGATTACTAAAATGGAGTTAAGTAGCGTAGAAGTTTTAGGAAAGGGATTATCGCCGAAGTTTTTGGCTAATACTTTAAGGCTAAATGCTGGGGTTGTATAGAATATATACAACACTGTCACAAAATGTGGAGAGCTATCATCTTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-95 nt.: TAAGATGATAGCTCTCCACATTTTGTGACAGTGTTGTATATATTCTATACAACCCCAGCATTTAGCCTTAAAGTATTAGCCAAAAACTTCGGCGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-95 nt.: AAAAGAGGTAGAGGCGCGAGAATCAAGATTACTAAAATGGAGTTAAGTAGCGTAGAAGTTTTAGGAAAGGGATTATCGCCGAAGTTTTTGGCTAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -19.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -22.81 kcal/mol. The frequency of the MFE structure in the ensemble is 0.24 %. The ensemble diversity is 36.00. The centroid secondary structure in dot-bracket notation with a minimum free energy of -9.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium perfringens , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

CT623541

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RiboSwitch type

Lysine type switch

Bacteria strain target

Clostridium tetani

Length of Switch in nucleotides

176

Sequence

TAGAAAGGTAGAGGCGCGGTATTTAATAGTATCTGTACAGATAAAAGCAAGATGATGTACAGTGAAAGGAAATATCGCCGAAGCATGCAGTTAAAGCTTTGATACTGTATGACTGGTCTTATTTAAAATATGAATAAGATTGTCACAAAATGAATTTGTGGAGAGCTATCATTCAA

Above is displayed the nucleotide sequence of the Clostridium tetani , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 66 nt. 2) Cytosine(C) in the sequence= 20 nt. 3) Guanine(G) in the sequence= 40 nt. 4) Thiamine(T) in the sequence= 50 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 176 nt. 8) CG percentage of the sequence= 34.09% 9) *Melting temperature of the DNA based on the Wallace formula= 75.06oC 10) The entered DNA sequence(5-3) is-176 nt.: TAGAAAGGTAGAGGCGCGGTATTTAATAGTATCTGTACAGATAAAAGCAAGATGATGTACAGTGAAAGGAAATATCGCCGAAGCATGCAGTTAAAGCTTTGATACTGTATGACTGGTCTTATTTAAAATATGAATAAGATTGTCACAAAATGAATTTGTGGAGAGCTATCATTCAA 11) The complementary(Com) sequence(3-5) is-176 nt.: ATCTTTCCATCTCCGCGCCATAAATTATCATAGACATGTCTATTTTCGTTCTACTACATGTCACTTTCCTTTATAGCGGCTTCGTACGTCAATTTCGAAACTATGACATACTGACCAGAATAAATTTTATACTTATTCTAACAGTGTTTTACTTAAACACCTCTCGATAGTAAGTT 12) The reverse(Rev) sequence(3-5) is-176 nt.: AACTTACTATCGAGAGGTGTTTAAGTAAAACACTGTTAGAATAAGTATAAAATTTATTCTGGTCAGTATGTCATAGTTTCGAAATTGACGTACGAAGCCGCTATAAAGGAAAGTGACATGTAGTAGAACGAAAATAGACATGTCTATGATAATTTATGGCGCGGAGATGGAAAGAT 13) The RevCom sequence(5-3) is-176 nt.: TTGAATGATAGCTCTCCACAAATTCATTTTGTGACAATCTTATTCATATTTTAAATAAGACCAGTCATACAGTATCAAAGCTTTAACTGCATGCTTCGGCGATATTTCCTTTCACTGTACATCATCTTGCTTTTATCTGTACAGATACTATTAAATACCGCGCCTCTACCTTTCTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-98 nt.: TAGAAAGGTAGAGGCGCGGTATTTAATAGTATCTGTACAGATAAAAGCAAGATGATGTACAGTGAAAGGAAATATCGCCGAAGCATGCAGTTAAAGCT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-98 nt.: TTGAATGATAGCTCTCCACAAATTCATTTTGTGACAATCTTATTCATATTTTAAATAAGACCAGTCATACAGTATCAAAGCTTTAACTGCATGCTTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -45.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -48.05 kcal/mol. The frequency of the MFE structure in the ensemble is 2.62 %. The ensemble diversity is 9.66. The centroid secondary structure in dot-bracket notation with a minimum free energy of -45.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

EF724180

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RiboSwitch type

Lysine type switch

Bacteria strain target

Enterococcus faecalis

Length of Switch in nucleotides

174

Sequence

AATGAGGTAGAGGTCGCGAGAATCATTAAACTTGTGGAGTGAAGCAAACACGTCGAAGCAAGGCTAGGGAGGATCGCCGAAATGTAAACTTTTTTGCTTGGAGTTTATGTTGGGACGTAAGTTAACAGCTTACGGACTGTCTTAGCAGTGATGCTAAGTTGCGCTATGTTTTGT

Above is displayed the nucleotide sequence of the Enterococcus faecalis , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 48 nt. 2) Cytosine(C) in the sequence= 25 nt. 3) Guanine(G) in the sequence= 51 nt. 4) Thiamine(T) in the sequence= 50 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 174 nt. 8) CG percentage of the sequence= 43.68% 9) *Melting temperature of the DNA based on the Wallace formula= 78.94oC 10) The entered DNA sequence(5-3) is-174 nt.: AATGAGGTAGAGGTCGCGAGAATCATTAAACTTGTGGAGTGAAGCAAACACGTCGAAGCAAGGCTAGGGAGGATCGCCGAAATGTAAACTTTTTTGCTTGGAGTTTATGTTGGGACGTAAGTTAACAGCTTACGGACTGTCTTAGCAGTGATGCTAAGTTGCGCTATGTTTTGT 11) The complementary(Com) sequence(3-5) is-174 nt.: TTACTCCATCTCCAGCGCTCTTAGTAATTTGAACACCTCACTTCGTTTGTGCAGCTTCGTTCCGATCCCTCCTAGCGGCTTTACATTTGAAAAAACGAACCTCAAATACAACCCTGCATTCAATTGTCGAATGCCTGACAGAATCGTCACTACGATTCAACGCGATACAAAACA 12) The reverse(Rev) sequence(3-5) is-174 nt.: TGTTTTGTATCGCGTTGAATCGTAGTGACGATTCTGTCAGGCATTCGACAATTGAATGCAGGGTTGTATTTGAGGTTCGTTTTTTCAAATGTAAAGCCGCTAGGAGGGATCGGAACGAAGCTGCACAAACGAAGTGAGGTGTTCAAATTACTAAGAGCGCTGGAGATGGAGTAA 13) The RevCom sequence(5-3) is-174 nt.: ACAAAACATAGCGCAACTTAGCATCACTGCTAAGACAGTCCGTAAGCTGTTAACTTACGTCCCAACATAAACTCCAAGCAAAAAAGTTTACATTTCGGCGATCCTCCCTAGCCTTGCTTCGACGTGTTTGCTTCACTCCACAAGTTTAATGATTCTCGCGACCTCTACCTCATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-97 nt.: AATGAGGTAGAGGTCGCGAGAATCATTAAACTTGTGGAGTGAAGCAAACACGTCGAAGCAAGGCTAGGGAGGATCGCCGAAATGTAAACTTTTTTGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-97 nt.: ACAAAACATAGCGCAACTTAGCATCACTGCTAAGACAGTCCGTAAGCTGTTAACTTACGTCCCAACATAAACTCCAAGCAAAAAAGTTTACATTTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecalis , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecalis , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -47.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -50.16 kcal/mol. The frequency of the MFE structure in the ensemble is 0.70 %. The ensemble diversity is 13.04. The centroid secondary structure in dot-bracket notation with a minimum free energy of -46.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecalis , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecalis , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

EF1085042

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RiboSwitch type

Lysine type switch

Bacteria strain target

Enterococcus faecium

Length of Switch in nucleotides

175

Sequence

ACAAAACATAGCGCAACTTAGCATCACTGCTAAGACAGTCCGCAAGCTCTTAACTTGCGTCCCAACATACACTCCAAGCAAAAAAGTGCACATTTCGGCGATCCTCCCTATTCCTGCTTCTCCATGTTTGCTTCACTCCACAGGGTTAATGATTCTCGCGACCTCTACCTCATTG

Above is displayed the nucleotide sequence of the Enterococcus faecium , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 47 nt. 2) Cytosine(C) in the sequence= 56 nt. 3) Guanine(G) in the sequence= 26 nt. 4) Thiamine(T) in the sequence= 46 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 175 nt. 8) CG percentage of the sequence= 46.86% 9) *Melting temperature of the DNA based on the Wallace formula= 80.27oC 10) The entered DNA sequence(5-3) is-175 nt.: ACAAAACATAGCGCAACTTAGCATCACTGCTAAGACAGTCCGCAAGCTCTTAACTTGCGTCCCAACATACACTCCAAGCAAAAAAGTGCACATTTCGGCGATCCTCCCTATTCCTGCTTCTCCATGTTTGCTTCACTCCACAGGGTTAATGATTCTCGCGACCTCTACCTCATTG 11) The complementary(Com) sequence(3-5) is-175 nt.: TGTTTTGTATCGCGTTGAATCGTAGTGACGATTCTGTCAGGCGTTCGAGAATTGAACGCAGGGTTGTATGTGAGGTTCGTTTTTTCACGTGTAAAGCCGCTAGGAGGGATAAGGACGAAGAGGTACAAACGAAGTGAGGTGTCCCAATTACTAAGAGCGCTGGAGATGGAGTAAC 12) The reverse(Rev) sequence(3-5) is-175 nt.: GTTACTCCATCTCCAGCGCTCTTAGTAATTGGGACACCTCACTTCGTTTGTACCTCTTCGTCCTTATCCCTCCTAGCGGCTTTACACGTGAAAAAACGAACCTCACATACAACCCTGCGTTCAATTCTCGAACGCCTGACAGAATCGTCACTACGATTCAACGCGATACAAAACA 13) The RevCom sequence(5-3) is-175 nt.: CAATGAGGTAGAGGTCGCGAGAATCATTAACCCTGTGGAGTGAAGCAAACATGGAGAAGCAGGAATAGGGAGGATCGCCGAAATGTGCACTTTTTTGCTTGGAGTGTATGTTGGGACGCAAGTTAAGAGCTTGCGGACTGTCTTAGCAGTGATGCTAAGTTGCGCTATGTTTTGT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-98 nt.: ACAAAACATAGCGCAACTTAGCATCACTGCTAAGACAGTCCGCAAGCTCTTAACTTGCGTCCCAACATACACTCCAAGCAAAAAAGTGCACATTTCGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-98 nt.: CAATGAGGTAGAGGTCGCGAGAATCATTAACCCTGTGGAGTGAAGCAAACATGGAGAAGCAGGAATAGGGAGGATCGCCGAAATGTGCACTTTTTTGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecium , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecium , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -28.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -30.67 kcal/mol. The frequency of the MFE structure in the ensemble is 1.55 %. The ensemble diversity is 31.83. The centroid secondary structure in dot-bracket notation with a minimum free energy of -14.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecium , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecium , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

KP512890

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RiboSwitch type

Lysine type switch

Bacteria strain target

Klebsiella pneumoniae

Length of Switch in nucleotides

236

Sequence

TCACCCAGAAGTGCTCCACCTTGTAGACCCGACTCACCGCTTTGGGCGCTGAGGTGTTCGGGTATGAAACGCCCGACTGCGAACGTTTCTGGTGACAACCCAGGGGATTCAGCCCCTGTGGCCGGCGAGGAGCGTGACCAGACGCTCTTTCACCTCGGCGTTGCTCCCCCTCACGTATCTTCCCCGGACTGGTTCCTCCAATACGGTTACCTGGGCAACGCACCTCTTCTGGCAAT

Above is displayed the nucleotide sequence of the Klebsiella pneumoniae , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 41 nt. 2) Cytosine(C) in the sequence= 80 nt. 3) Guanine(G) in the sequence= 62 nt. 4) Thiamine(T) in the sequence= 53 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 236 nt. 8) CG percentage of the sequence= 60.17% 9) *Melting temperature of the DNA based on the Wallace formula= 86.72oC 10) The entered DNA sequence(5-3) is-236 nt.: TCACCCAGAAGTGCTCCACCTTGTAGACCCGACTCACCGCTTTGGGCGCTGAGGTGTTCGGGTATGAAACGCCCGACTGCGAACGTTTCTGGTGACAACCCAGGGGATTCAGCCCCTGTGGCCGGCGAGGAGCGTGACCAGACGCTCTTTCACCTCGGCGTTGCTCCCCCTCACGTATCTTCCCCGGACTGGTTCCTCCAATACGGTTACCTGGGCAACGCACCTCTTCTGGCAAT 11) The complementary(Com) sequence(3-5) is-236 nt.: AGTGGGTCTTCACGAGGTGGAACATCTGGGCTGAGTGGCGAAACCCGCGACTCCACAAGCCCATACTTTGCGGGCTGACGCTTGCAAAGACCACTGTTGGGTCCCCTAAGTCGGGGACACCGGCCGCTCCTCGCACTGGTCTGCGAGAAAGTGGAGCCGCAACGAGGGGGAGTGCATAGAAGGGGCCTGACCAAGGAGGTTATGCCAATGGACCCGTTGCGTGGAGAAGACCGTTA 12) The reverse(Rev) sequence(3-5) is-236 nt.: TAACGGTCTTCTCCACGCAACGGGTCCATTGGCATAACCTCCTTGGTCAGGCCCCTTCTATGCACTCCCCCTCGTTGCGGCTCCACTTTCTCGCAGACCAGTGCGAGGAGCGGCCGGTGTCCCCGACTTAGGGGACCCAACAGTGGTCTTTGCAAGCGTCAGCCCGCAAAGTATGGGCTTGTGGAGTCGCGGGTTTCGCCACTCAGCCCAGATGTTCCACCTCGTGAAGACCCACT 13) The RevCom sequence(5-3) is-236 nt.: ATTGCCAGAAGAGGTGCGTTGCCCAGGTAACCGTATTGGAGGAACCAGTCCGGGGAAGATACGTGAGGGGGAGCAACGCCGAGGTGAAAGAGCGTCTGGTCACGCTCCTCGCCGGCCACAGGGGCTGAATCCCCTGGGTTGTCACCAGAAACGTTCGCAGTCGGGCGTTTCATACCCGAACACCTCAGCGCCCAAAGCGGTGAGTCGGGTCTACAAGGTGGAGCACTTCTGGGTGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-128 nt.: TCACCCAGAAGTGCTCCACCTTGTAGACCCGACTCACCGCTTTGGGCGCTGAGGTGTTCGGGTATGAAACGCCCGACTGCGAACGTTTCTGGTGACAACCCAGGGGATTCAGCCCCTGTGGCCGGCGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-128 nt.: ATTGCCAGAAGAGGTGCGTTGCCCAGGTAACCGTATTGGAGGAACCAGTCCGGGGAAGATACGTGAGGGGGAGCAACGCCGAGGTGAAAGAGCGTCTGGTCACGCTCCTCGCCGGCCACAGGGGCTGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Klebsiella pneumoniae , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Klebsiella pneumoniae , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -86.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -89.55 kcal/mol. The frequency of the MFE structure in the ensemble is 0.83 %. The ensemble diversity is 29.93. The centroid secondary structure in dot-bracket notation with a minimum free energy of -81.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Klebsiella pneumoniae , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Klebsiella pneumoniae , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

LM725689

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RiboSwitch type

Lysine type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

236

Sequence

TTGTCAGATAGCACACCTATAAGAAATTTCGACAAATTCTTATAGCAGTCCAGCCCCTTTAGGAAACTGTCCCAACAACTATTTCTAAACAAAGAGAAAATAGTCACTTCGGCGATCAACCTGTTCATTCTTTGTCGTCGGCGTCTTTGTTTCGCCTCGAAAAAATTACTAGTGCATCTCGCAACCTCTACCTCACCA

Above is displayed the nucleotide sequence of the Listeria monocytogenes , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 59 nt. 2) Cytosine(C) in the sequence= 53 nt. 3) Guanine(G) in the sequence= 29 nt. 4) Thiamine(T) in the sequence= 57 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 198 nt. 8) CG percentage of the sequence= 41.41% 9) *Melting temperature of the DNA based on the Wallace formula= 78.48oC 10) The entered DNA sequence(5-3) is-198 nt.: TTGTCAGATAGCACACCTATAAGAAATTTCGACAAATTCTTATAGCAGTCCAGCCCCTTTAGGAAACTGTCCCAACAACTATTTCTAAACAAAGAGAAAATAGTCACTTCGGCGATCAACCTGTTCATTCTTTGTCGTCGGCGTCTTTGTTTCGCCTCGAAAAAATTACTAGTGCATCTCGCAACCTCTACCTCACCA 11) The complementary(Com) sequence(3-5) is-198 nt.: AACAGTCTATCGTGTGGATATTCTTTAAAGCTGTTTAAGAATATCGTCAGGTCGGGGAAATCCTTTGACAGGGTTGTTGATAAAGATTTGTTTCTCTTTTATCAGTGAAGCCGCTAGTTGGACAAGTAAGAAACAGCAGCCGCAGAAACAAAGCGGAGCTTTTTTAATGATCACGTAGAGCGTTGGAGATGGAGTGGT 12) The reverse(Rev) sequence(3-5) is-198 nt.: ACCACTCCATCTCCAACGCTCTACGTGATCATTAAAAAAGCTCCGCTTTGTTTCTGCGGCTGCTGTTTCTTACTTGTCCAACTAGCGGCTTCACTGATAAAAGAGAAACAAATCTTTATCAACAACCCTGTCAAAGGATTTCCCCGACCTGACGATATTCTTAAACAGCTTTAAAGAATATCCACACGATAGACTGTT 13) The RevCom sequence(5-3) is-198 nt.: TGGTGAGGTAGAGGTTGCGAGATGCACTAGTAATTTTTTCGAGGCGAAACAAAGACGCCGACGACAAAGAATGAACAGGTTGATCGCCGAAGTGACTATTTTCTCTTTGTTTAGAAATAGTTGTTGGGACAGTTTCCTAAAGGGGCTGGACTGCTATAAGAATTTGTCGAAATTTCTTATAGGTGTGCTATCTGACAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-109 nt.: TTGTCAGATAGCACACCTATAAGAAATTTCGACAAATTCTTATAGCAGTCCAGCCCCTTTAGGAAACTGTCCCAACAACTATTTCTAAACAAAGAGAAAATAGTCACTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-109 nt.: TGGTGAGGTAGAGGTTGCGAGATGCACTAGTAATTTTTTCGAGGCGAAACAAAGACGCCGACGACAAAGAATGAACAGGTTGATCGCCGAAGTGACTATTTTCTCTTTG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -37.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -42.63 kcal/mol. The frequency of the MFE structure in the ensemble is 0.05 %. The ensemble diversity is 28.82. The centroid secondary structure in dot-bracket notation with a minimum free energy of -29.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

SA182560

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RiboSwitch type

Lysine type switch

Bacteria strain target

Staphylococcus aureus

Length of Switch in nucleotides

176

Sequence

ATATAAGGTAGCACATCACATTCTGTGACAGTACAGTTCCTATTCGAAAACTGTCCCAATAGATATAATTTATGGTTTATATCTATTTCGGCATCTTTACCTTTCACTTGTTCAACTTATGTACCATAAATACTTCTGACAAGTTACTAATTAAACATGCAACCTCTAACTCAATT

Above is displayed the nucleotide sequence of the Staphylococcus aureus , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 57 nt. 2) Cytosine(C) in the sequence= 37 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 63 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 176 nt. 8) CG percentage of the sequence= 31.82% 9) *Melting temperature of the DNA based on the Wallace formula= 74.12oC 10) The entered DNA sequence(5-3) is-176 nt.: ATATAAGGTAGCACATCACATTCTGTGACAGTACAGTTCCTATTCGAAAACTGTCCCAATAGATATAATTTATGGTTTATATCTATTTCGGCATCTTTACCTTTCACTTGTTCAACTTATGTACCATAAATACTTCTGACAAGTTACTAATTAAACATGCAACCTCTAACTCAATT 11) The complementary(Com) sequence(3-5) is-176 nt.: TATATTCCATCGTGTAGTGTAAGACACTGTCATGTCAAGGATAAGCTTTTGACAGGGTTATCTATATTAAATACCAAATATAGATAAAGCCGTAGAAATGGAAAGTGAACAAGTTGAATACATGGTATTTATGAAGACTGTTCAATGATTAATTTGTACGTTGGAGATTGAGTTAA 12) The reverse(Rev) sequence(3-5) is-176 nt.: TTAACTCAATCTCCAACGTACAAATTAATCATTGAACAGTCTTCATAAATACCATGTATTCAACTTGTTCACTTTCCATTTCTACGGCTTTATCTATATTTGGTATTTAATATAGATAACCCTGTCAAAAGCTTATCCTTGACATGACAGTGTCTTACACTACACGATGGAATATA 13) The RevCom sequence(5-3) is-176 nt.: AATTGAGTTAGAGGTTGCATGTTTAATTAGTAACTTGTCAGAAGTATTTATGGTACATAAGTTGAACAAGTGAAAGGTAAAGATGCCGAAATAGATATAAACCATAAATTATATCTATTGGGACAGTTTTCGAATAGGAACTGTACTGTCACAGAATGTGATGTGCTACCTTATAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-98 nt.: ATATAAGGTAGCACATCACATTCTGTGACAGTACAGTTCCTATTCGAAAACTGTCCCAATAGATATAATTTATGGTTTATATCTATTTCGGCATCTTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-98 nt.: AATTGAGTTAGAGGTTGCATGTTTAATTAGTAACTTGTCAGAAGTATTTATGGTACATAAGTTGAACAAGTGAAAGGTAAAGATGCCGAAATAGATAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -28.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -32.30 kcal/mol. The frequency of the MFE structure in the ensemble is 0.25 %. The ensemble diversity is 24.78. The centroid secondary structure in dot-bracket notation with a minimum free energy of -25.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

SE913520

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RiboSwitch type

Lysine type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

176

Sequence

ATATAAGGTAGCACATCACATAAAGTGACAGTACAACTTCTATTCGAAAGTTGTCCCAACAATGCTAATTTATGGAAATAACATCATTTCGGCATTATTACCTTTCACTTATTCAACACATGTCCCATACGACTTCTGATAAGTTAGTCATTAATAATGCAACCTCTAACTCTATT

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 61 nt. 2) Cytosine(C) in the sequence= 38 nt. 3) Guanine(G) in the sequence= 20 nt. 4) Thiamine(T) in the sequence= 57 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 176 nt. 8) CG percentage of the sequence= 32.95% 9) *Melting temperature of the DNA based on the Wallace formula= 74.59oC 10) The entered DNA sequence(5-3) is-176 nt.: ATATAAGGTAGCACATCACATAAAGTGACAGTACAACTTCTATTCGAAAGTTGTCCCAACAATGCTAATTTATGGAAATAACATCATTTCGGCATTATTACCTTTCACTTATTCAACACATGTCCCATACGACTTCTGATAAGTTAGTCATTAATAATGCAACCTCTAACTCTATT 11) The complementary(Com) sequence(3-5) is-176 nt.: TATATTCCATCGTGTAGTGTATTTCACTGTCATGTTGAAGATAAGCTTTCAACAGGGTTGTTACGATTAAATACCTTTATTGTAGTAAAGCCGTAATAATGGAAAGTGAATAAGTTGTGTACAGGGTATGCTGAAGACTATTCAATCAGTAATTATTACGTTGGAGATTGAGATAA 12) The reverse(Rev) sequence(3-5) is-176 nt.: TTATCTCAATCTCCAACGTAATAATTACTGATTGAATAGTCTTCAGCATACCCTGTACACAACTTATTCACTTTCCATTATTACGGCTTTACTACAATAAAGGTATTTAATCGTAACAACCCTGTTGAAAGCTTATCTTCAACATGACAGTGAAATACACTACACGATGGAATATA 13) The RevCom sequence(5-3) is-176 nt.: AATAGAGTTAGAGGTTGCATTATTAATGACTAACTTATCAGAAGTCGTATGGGACATGTGTTGAATAAGTGAAAGGTAATAATGCCGAAATGATGTTATTTCCATAAATTAGCATTGTTGGGACAACTTTCGAATAGAAGTTGTACTGTCACTTTATGTGATGTGCTACCTTATAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-98 nt.: ATATAAGGTAGCACATCACATAAAGTGACAGTACAACTTCTATTCGAAAGTTGTCCCAACAATGCTAATTTATGGAAATAACATCATTTCGGCATTAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-98 nt.: AATAGAGTTAGAGGTTGCATTATTAATGACTAACTTATCAGAAGTCGTATGGGACATGTGTTGAATAAGTGAAAGGTAATAATGCCGAAATGATGTTA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis , Lysine type switch.

2D_Structure (A) (B)

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

StS341234

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RiboSwitch type

Lysine type switch

Bacteria strain target

Staphylococcus saprophyticus

Length of Switch in nucleotides

173

Sequence

ATTTGAGTTAGAGGTTGCGTTTTTAAAGAGTAATGATTCAGAAGCCAGATGGGGCATATGTTGAATGCATGAAAGGTGAAAATGCCGAAACCTGTATTGACCATTTACAATACAGGTTGGGACAGTTATCGAAAGAAACTGGACTGTCACATATGTGATGTGCTACCTATATA

Above is displayed the nucleotide sequence of the Staphylococcus saprophyticus , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 57 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 43 nt. 4) Thiamine(T) in the sequence= 50 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 173 nt. 8) CG percentage of the sequence= 38.15% 9) *Melting temperature of the DNA based on the Wallace formula= 76.65oC 10) The entered DNA sequence(5-3) is-173 nt.: ATTTGAGTTAGAGGTTGCGTTTTTAAAGAGTAATGATTCAGAAGCCAGATGGGGCATATGTTGAATGCATGAAAGGTGAAAATGCCGAAACCTGTATTGACCATTTACAATACAGGTTGGGACAGTTATCGAAAGAAACTGGACTGTCACATATGTGATGTGCTACCTATATA 11) The complementary(Com) sequence(3-5) is-173 nt.: TAAACTCAATCTCCAACGCAAAAATTTCTCATTACTAAGTCTTCGGTCTACCCCGTATACAACTTACGTACTTTCCACTTTTACGGCTTTGGACATAACTGGTAAATGTTATGTCCAACCCTGTCAATAGCTTTCTTTGACCTGACAGTGTATACACTACACGATGGATATAT 12) The reverse(Rev) sequence(3-5) is-173 nt.: ATATATCCATCGTGTAGTGTATACACTGTCAGGTCAAAGAAAGCTATTGACAGGGTTGGACATAACATTTACCAGTTATGTCCAAAGCCGTAAAAGTGGAAAGTACGTAAGTTGTATACGGGGTAGACCGAAGACTTAGTAATGAGAAATTTTTGCGTTGGAGATTGAGTTTA 13) The RevCom sequence(5-3) is-173 nt.: TATATAGGTAGCACATCACATATGTGACAGTCCAGTTTCTTTCGATAACTGTCCCAACCTGTATTGTAAATGGTCAATACAGGTTTCGGCATTTTCACCTTTCATGCATTCAACATATGCCCCATCTGGCTTCTGAATCATTACTCTTTAAAAACGCAACCTCTAACTCAAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-97 nt.: ATTTGAGTTAGAGGTTGCGTTTTTAAAGAGTAATGATTCAGAAGCCAGATGGGGCATATGTTGAATGCATGAAAGGTGAAAATGCCGAAACCTGTAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-97 nt.: TATATAGGTAGCACATCACATATGTGACAGTCCAGTTTCTTTCGATAACTGTCCCAACCTGTATTGTAAATGGTCAATACAGGTTTCGGCATTTTCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus saprophyticus , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus saprophyticus , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -47.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -49.10 kcal/mol. The frequency of the MFE structure in the ensemble is 6.37 %. The ensemble diversity is 35.62. The centroid secondary structure in dot-bracket notation with a minimum free energy of -34.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus saprophyticus , Lysine type switch.

2D_Structure (A) (B)

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

VC712402

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RiboSwitch type

Lysine type switch

Bacteria strain target

Vibrio cholerae

Length of Switch in nucleotides

173

Sequence

CTTCAAGGTAGCGCTCCATAGACAACACACTATGGCAGTCCGGCATTTGTTCAATGCTGGCCCAGCGAACGTTGATGACGCAACGATCACTTCGGCGCTGTACCCTTTAACCAGTCATCATCGGGGTCAACCTACGACTGGCGACTCATGAACAGCGCGCCTCTACTTAAAGG

Above is displayed the nucleotide sequence of the Vibrio cholerae , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 43 nt. 2) Cytosine(C) in the sequence= 52 nt. 3) Guanine(G) in the sequence= 40 nt. 4) Thiamine(T) in the sequence= 38 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 173 nt. 8) CG percentage of the sequence= 53.18% 9) *Melting temperature of the DNA based on the Wallace formula= 82.82oC 10) The entered DNA sequence(5-3) is-173 nt.: CTTCAAGGTAGCGCTCCATAGACAACACACTATGGCAGTCCGGCATTTGTTCAATGCTGGCCCAGCGAACGTTGATGACGCAACGATCACTTCGGCGCTGTACCCTTTAACCAGTCATCATCGGGGTCAACCTACGACTGGCGACTCATGAACAGCGCGCCTCTACTTAAAGG 11) The complementary(Com) sequence(3-5) is-173 nt.: GAAGTTCCATCGCGAGGTATCTGTTGTGTGATACCGTCAGGCCGTAAACAAGTTACGACCGGGTCGCTTGCAACTACTGCGTTGCTAGTGAAGCCGCGACATGGGAAATTGGTCAGTAGTAGCCCCAGTTGGATGCTGACCGCTGAGTACTTGTCGCGCGGAGATGAATTTCC 12) The reverse(Rev) sequence(3-5) is-173 nt.: GGAAATTCATCTCCGCGCGACAAGTACTCAGCGGTCAGCATCCAACTGGGGCTACTACTGACCAATTTCCCATGTCGCGGCTTCACTAGCAACGCAGTAGTTGCAAGCGACCCGGTCGTAACTTGTTTACGGCCTGACGGTATCACACAACAGATACCTCGCGATGGAACTTC 13) The RevCom sequence(5-3) is-173 nt.: CCTTTAAGTAGAGGCGCGCTGTTCATGAGTCGCCAGTCGTAGGTTGACCCCGATGATGACTGGTTAAAGGGTACAGCGCCGAAGTGATCGTTGCGTCATCAACGTTCGCTGGGCCAGCATTGAACAAATGCCGGACTGCCATAGTGTGTTGTCTATGGAGCGCTACCTTGAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-97 nt.: CTTCAAGGTAGCGCTCCATAGACAACACACTATGGCAGTCCGGCATTTGTTCAATGCTGGCCCAGCGAACGTTGATGACGCAACGATCACTTCGGCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-97 nt.: CCTTTAAGTAGAGGCGCGCTGTTCATGAGTCGCCAGTCGTAGGTTGACCCCGATGATGACTGGTTAAAGGGTACAGCGCCGAAGTGATCGTTGCGTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Vibrio cholerae , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Vibrio cholerae , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -51.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -54.20 kcal/mol. The frequency of the MFE structure in the ensemble is 1.24 %. The ensemble diversity is 28.54. The centroid secondary structure in dot-bracket notation with a minimum free energy of -48.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Vibrio cholerae , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Vibrio cholerae , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

EC182064

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RiboSwitch type

Lysine type switch

Bacteria strain target

Escherichia coli

Length of Switch in nucleotides

197

Sequence

TCACCCAGAAGTGCTCCACCACTTGCGAAACGCCCGACTGCGAACGCTTCTGGTGACAACCCAGGGGATTCAGCCCCTGTAGCCGATGATGAACGTGGCCAGCCGTTCAATCACCTCGGCGATGCACCCCCTCAGGTGTTATCACAGGACTGGCTCCTCCAACACCGTTACTTGGCAACGCGCCTCTTCTGGCCTG

Above is displayed the nucleotide sequence of the Escherichia coli , Lysine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 40 nt. 2) Cytosine(C) in the sequence= 70 nt. 3) Guanine(G) in the sequence= 48 nt. 4) Thiamine(T) in the sequence= 39 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 197 nt. 8) CG percentage of the sequence= 59.90% 9) *Melting temperature of the DNA based on the Wallace formula= 86.05oC 10) The entered DNA sequence(5-3) is-197 nt.: TCACCCAGAAGTGCTCCACCACTTGCGAAACGCCCGACTGCGAACGCTTCTGGTGACAACCCAGGGGATTCAGCCCCTGTAGCCGATGATGAACGTGGCCAGCCGTTCAATCACCTCGGCGATGCACCCCCTCAGGTGTTATCACAGGACTGGCTCCTCCAACACCGTTACTTGGGCAACGCGCCTCTTCTGGCCTG 11) The complementary(Com) sequence(3-5) is-197 nt.: AGTGGGTCTTCACGAGGTGGTGAACGCTTTGCGGGCTGACGCTTGCGAAGACCACTGTTGGGTCCCCTAAGTCGGGGACATCGGCTACTACTTGCACCGGTCGGCAAGTTAGTGGAGCCGCTACGTGGGGGAGTCCACAATAGTGTCCTGACCGAGGAGGTTGTGGCAATGAACCCGTTGCGCGGAGAAGACCGGAC 12) The reverse(Rev) sequence(3-5) is-197 nt.: GTCCGGTCTTCTCCGCGCAACGGGTTCATTGCCACAACCTCCTCGGTCAGGACACTATTGTGGACTCCCCCACGTAGCGGCTCCACTAACTTGCCGACCGGTGCAAGTAGTAGCCGATGTCCCCGACTTAGGGGACCCAACAGTGGTCTTCGCAAGCGTCAGCCCGCAAAGCGTTCACCACCTCGTGAAGACCCACT 13) The RevCom sequence(5-3) is-197 nt.: CAGGCCAGAAGAGGCGCGTTGCCCAAGTAACGGTGTTGGAGGAGCCAGTCCTGTGATAACACCTGAGGGGGTGCATCGCCGAGGTGATTGAACGGCTGGCCACGTTCATCATCGGCTACAGGGGCTGAATCCCCTGGGTTGTCACCAGAAGCGTTCGCAGTCGGGCGTTTCGCAAGTGGTGGAGCACTTCTGGGTGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-109 nt.: TCACCCAGAAGTGCTCCACCACTTGCGAAACGCCCGACTGCGAACGCTTCTGGTGACAACCCAGGGGATTCAGCCCCTGTAGCCGATGATGAACGTGGCCAGCCGTTCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-109 nt.: CAGGCCAGAAGAGGCGCGTTGCCCAAGTAACGGTGTTGGAGGAGCCAGTCCTGTGATAACACCTGAGGGGGTGCATCGCCGAGGTGATTGAACGGCTGGCCACGTTCAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Escherichia coli , Lysine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Escherichia coli , Lysine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -66.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -69.40 kcal/mol. The frequency of the MFE structure in the ensemble is 0.56 %. The ensemble diversity is 42.23. The centroid secondary structure in dot-bracket notation with a minimum free energy of -55.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Escherichia coli , Lysine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Escherichia coli , Lysine type switch.

Multiple alignment of the Lysine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Lysine type switches involved in.

Multi_resistance strains for the Lysine type switches

RiboSwitch_ID:

BPE27790

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RiboSwitch type

SAH type switch

Bacteria strain target

Bordetella pertussis

Length of Switch in nucleotides

121

Sequence

CAAAGGTGAGCGCCGTTGCTGCGGCGCCGCGCGATGTGCGGCGCGTGAACAAGGATTTCCTGAGCCTGGCGACCGGCATGCCGTGGACACGGCCCGGGTCGTCGCAGCGCTCCTCAGGAAT

Above is displayed the nucleotide sequence of the Bordetella pertussis , SAH type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 19 nt. 2) Cytosine(C) in the sequence= 38 nt. 3) Guanine(G) in the sequence= 45 nt. 4) Thiamine(T) in the sequence= 19 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 121 nt. 8) CG percentage of the sequence= 68.60% 9) *Melting temperature of the DNA based on the Wallace formula= 87.47oC 10) The entered DNA sequence(5-3) is-121 nt.: CAAAGGTGAGCGCCGTTGCTGCGGCGCCGCGCGATGTGCGGCGCGTGAACAAGGATTTCCTGAGCCTGGCGACCGGCATGCCGTGGACACGGCCCGGGTCGTCGCAGCGCTCCTCAGGAAT 11) The complementary(Com) sequence(3-5) is-121 nt.: GTTTCCACTCGCGGCAACGACGCCGCGGCGCGCTACACGCCGCGCACTTGTTCCTAAAGGACTCGGACCGCTGGCCGTACGGCACCTGTGCCGGGCCCAGCAGCGTCGCGAGGAGTCCTTA 12) The reverse(Rev) sequence(3-5) is-121 nt.: TAAGGACTCCTCGCGACGCTGCTGGGCCCGGCACAGGTGCCGTACGGCCAGCGGTCCGAGTCCTTTAGGAACAAGTGCGCGGCGTGTAGCGCGCCGCGGCGTCGTTGCCGCGAGTGGAAAC 13) The RevCom sequence(5-3) is-121 nt.: ATTCCTGAGGAGCGCTGCGACGACCCGGGCCGTGTCCACGGCATGCCGGTCGCCAGGCTCAGGAAATCCTTGTTCACGCGCCGCACATCGCGCGGCGCCGCAGCAACGGCGCTCACCTTTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-71 nt.: CAAAGGTGAGCGCCGTTGCTGCGGCGCCGCGCGATGTGCGGCGCGTGAACAAGGATTTCCTGAGCCTGGCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-71 nt.: ATTCCTGAGGAGCGCTGCGACGACCCGGGCCGTGTCCACGGCATGCCGGTCGCCAGGCTCAGGAAATCCTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bordetella pertussis , SAH type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bordetella pertussis , SAH type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bordetella pertussis , SAH type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bordetella pertussis , SAH type switch.

Multiple alignment of the SAH type switches

Below is presented the sequences alignment of all the SAH type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the SAH type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the SAH riboswitches and shorter motifs based on the general one: 1) N{0,6}YCRCAACGGCTTCCTGRCGYGRN{0,9}YN{0,2}AN?TGGAGCA 2) YCRCAACGGCTTCCTGRCGYGR 3) TGGAGCA Motifs identified amongst the SAH riboswitches based on the sequences alignment: 1) TGRGCGCCGTTGSTGCG 2) GCGCCGTTG 3) GACMGGCMT Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the SAH type switches involved in.

Multi_resistance strains for the SAH type switches

The table displays known human pathogenic bacteria bearing the SAH type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

PA441211

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RiboSwitch type

SAH type switch

Bacteria strain target

Pseudomonas aeruginosa

Length of Switch in nucleotides

106

Sequence

TGCGAATGGGCGCCGTTGGTGCGTTGACAGACCGGCGAGGCCGGCCTGAGAGCGCGCTCCGTTCGAGCCTGACAGGCCTAGGCCTGCTGCAGCGCCCCTCGAACGG

Above is displayed the nucleotide sequence of the Pseudomonas aeruginosa , SAH type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 15 nt. 2) Cytosine(C) in the sequence= 35 nt. 3) Guanine(G) in the sequence= 40 nt. 4) Thiamine(T) in the sequence= 16 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 70.75% 9) *Melting temperature of the DNA based on the Wallace formula= 87.57oC 10) The entered DNA sequence(5-3) is-106 nt.: TGCGAATGGGCGCCGTTGGTGCGTTGACAGACCGGCGAGGCCGGCCTGAGAGCGCGCTCCGTTCGAGCCTGACAGGCCTAGGCCTGCTGCAGCGCCCCTCGAACGG 11) The complementary(Com) sequence(3-5) is-106 nt.: ACGCTTACCCGCGGCAACCACGCAACTGTCTGGCCGCTCCGGCCGGACTCTCGCGCGAGGCAAGCTCGGACTGTCCGGATCCGGACGACGTCGCGGGGAGCTTGCC 12) The reverse(Rev) sequence(3-5) is-106 nt.: GGCAAGCTCCCCGCGACGTCGTCCGGATCCGGACAGTCCGAGCTTGCCTCGCGCGAGAGTCCGGCCGGAGCGGCCAGACAGTTGCGTGGTTGCCGCGGGTAAGCGT 13) The RevCom sequence(5-3) is-106 nt.: CCGTTCGAGGGGCGCTGCAGCAGGCCTAGGCCTGTCAGGCTCGAACGGAGCGCGCTCTCAGGCCGGCCTCGCCGGTCTGTCAACGCACCAACGGCGCCCATTCGCA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: TGCGAATGGGCGCCGTTGGTGCGTTGACAGACCGGCGAGGCCGGCCTGAGAGCGCGCTCCGTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: CCGTTCGAGGGGCGCTGCAGCAGGCCTAGGCCTGTCAGGCTCGAACGGAGCGCGCTCTCAGGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Pseudomonas aeruginosa , SAH type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Pseudomonas aeruginosa , SAH type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -48.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -50.20 kcal/mol. The frequency of the MFE structure in the ensemble is 10.35 %. The ensemble diversity is 22.30. The centroid secondary structure in dot-bracket notation with a minimum free energy of -42.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Pseudomonas aeruginosa , SAH type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Pseudomonas aeruginosa , SAH type switch.

Multiple alignment of the SAH type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAH type switches involved in.

Multi_resistance strains for the SAH type switches

RiboSwitch_ID:

BA786211

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RiboSwitch type

SAM type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

110

Sequence

TTCTTATCTAGAGAGGTAGAGGGACTGGCCCTATGACGCCTCAGCAACCATTAACATTTGTTAATAAGGTGCTAATTCCAGCAAATTGCGAAAAATTTGACAGATGAGAA

Above is displayed the nucleotide sequence of the Bacillus anthracis, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 37 nt. 2) Cytosine(C) in the sequence= 20 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 110 nt. 8) CG percentage of the sequence= 40.00% 9) *Melting temperature of the DNA based on the Wallace formula= 75.19oC 10) The entered DNA sequence(5-3) is-110 nt.: TTCTTATCTAGAGAGGTAGAGGGACTGGCCCTATGACGCCTCAGCAACCATTAACATTTGTTAATAAGGTGCTAATTCCAGCAAATTGCGAAAAATTTGACAGATGAGAA 11) The complementary(Com) sequence(3-5) is-110 nt.: AAGAATAGATCTCTCCATCTCCCTGACCGGGATACTGCGGAGTCGTTGGTAATTGTAAACAATTATTCCACGATTAAGGTCGTTTAACGCTTTTTAAACTGTCTACTCTT 12) The reverse(Rev) sequence(3-5) is-110 nt.: AAGAGTAGACAGTTTAAAAAGCGTTAAACGACCTTAATCGTGGAATAATTGTTTACAATTACCAACGACTCCGCAGTATCCCGGTCAGGGAGATGGAGAGATCTATTCTT 13) The RevCom sequence(5-3) is-110 nt.: TTCTCATCTGTCAAATTTTTCGCAATTTGCTGGAATTAGCACCTTATTAACAAATGTTAATGGTTGCTGAGGCGTCATAGGGCCAGTCCCTCTACCTCTCTAGATAAGAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: TTCTTATCTAGAGAGGTAGAGGGACTGGCCCTATGACGCCTCAGCAACCATTAACATTTGTTAAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: TTCTCATCTGTCAAATTTTTCGCAATTTGCTGGAATTAGCACCTTATTAACAAATGTTAATGGTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -31.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -32.41 kcal/mol. The frequency of the MFE structure in the ensemble is 10.08 %. The ensemble diversity is 6.69. The centroid secondary structure in dot-bracket notation with a minimum free energy of -31.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis, SAM type switch.

Multiple alignment of the SAM type switches

Below is presented the sequences alignment of all the SAM type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the SAM type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the SAM riboswitches and shorter motifs based on the general one: 1) N{0,5}RCATYARGAGN?RN{0,5}RN{0,4}YN?YRN?CAACCN?R{0,10}CN?GGTGN?YN{0,4}GATGYGRYN{0,6}RYAAN{0,14} 2) RCATYARGAG 3) GATGYGRY Motifs identified amongst the SAM riboswitches based on the sequences alignment: 1) GBTGCT 2) TGCTAA 3) GATVAG 4) GGTTGCYGG 5) TCCCTCHRCCHCTCWKDATAA 6) GGTTGCYGGGYTTCAWMGGGC Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

The table displays known human pathogenic bacteria bearing the SAM type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BC532234

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RiboSwitch type

SAM type switch

Bacteria strain target

Bacillus cereus

Length of Switch in nucleotides

106

Sequence

TACTTATCCAGAGAGGTAGAGGGACTGGCCCTATGACACCTCAGCAGCGGGTTCTGTAATAGGAACACCGTGCTAATTCCAGCAAGCAAGTCTTGAAAGATAAGTG

Above is displayed the nucleotide sequence of the Bacillus cereus, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 28 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 48.11% 9) *Melting temperature of the DNA based on the Wallace formula= 78.28oC 10) The entered DNA sequence(5-3) is-106 nt.: TACTTATCCAGAGAGGTAGAGGGACTGGCCCTATGACACCTCAGCAGCGGGTTCTGTAATAGGAACACCGTGCTAATTCCAGCAAGCAAGTCTTGAAAGATAAGTG 11) The complementary(Com) sequence(3-5) is-106 nt.: ATGAATAGGTCTCTCCATCTCCCTGACCGGGATACTGTGGAGTCGTCGCCCAAGACATTATCCTTGTGGCACGATTAAGGTCGTTCGTTCAGAACTTTCTATTCAC 12) The reverse(Rev) sequence(3-5) is-106 nt.: GTGAATAGAAAGTTCTGAACGAACGACCTTAATCGTGCCACAAGGATAATGTCTTGGGCGACGACTCCACAGTATCCCGGTCAGGGAGATGGAGAGACCTATTCAT 13) The RevCom sequence(5-3) is-106 nt.: CACTTATCTTTCAAGACTTGCTTGCTGGAATTAGCACGGTGTTCCTATTACAGAACCCGCTGCTGAGGTGTCATAGGGCCAGTCCCTCTACCTCTCTGGATAAGTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: TACTTATCCAGAGAGGTAGAGGGACTGGCCCTATGACACCTCAGCAGCGGGTTCTGTAATAGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: CACTTATCTTTCAAGACTTGCTTGCTGGAATTAGCACGGTGTTCCTATTACAGAACCCGCTGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus cereus, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus cereus, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -32.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -34.20 kcal/mol. The frequency of the MFE structure in the ensemble is 12.06 %. The ensemble diversity is 10.51. The centroid secondary structure in dot-bracket notation with a minimum free energy of -32.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus cereus, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus cereus, SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

BS08906

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RiboSwitch type

SAM type switch

Bacteria strain target

Bacillus subtilis

Length of Switch in nucleotides

118

Sequence

TTCTTATCTTCCAAGCTGTTCGAGCTTGCTGGATTTAGCACCTTGGTCATGGCTGATCGCCATTACACCGGTTGCTGAAGCTTCGTCGGGCCAGTCCCTCTGCTTCTCTTGATAAGAA

Above is displayed the nucleotide sequence of the Bacillus subtilis , SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 32 nt. 3) Guanine(G) in the sequence= 27 nt. 4) Thiamine(T) in the sequence= 39 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 118 nt. 8) CG percentage of the sequence= 50.00% 9) *Melting temperature of the DNA based on the Wallace formula= 79.70oC 10) The entered DNA sequence(5-3) is-118 nt.: TTCTTATCTTCCAAGCTGTTCGAGCTTGCTGGATTTAGCACCTTGGTCATGGCTGATCGCCATTACACCGGTTGCTGAAGCTTCGTCGGGCCAGTCCCTCTGCTTCTCTTGATAAGAA 11) The complementary(Com) sequence(3-5) is-118 nt.: AAGAATAGAAGGTTCGACAAGCTCGAACGACCTAAATCGTGGAACCAGTACCGACTAGCGGTAATGTGGCCAACGACTTCGAAGCAGCCCGGTCAGGGAGACGAAGAGAACTATTCTT 12) The reverse(Rev) sequence(3-5) is-118 nt.: AAGAATAGTTCTCTTCGTCTCCCTGACCGGGCTGCTTCGAAGTCGTTGGCCACATTACCGCTAGTCGGTACTGGTTCCACGATTTAGGTCGTTCGAGCTTGTCGAACCTTCTATTCTT 13) The RevCom sequence(5-3) is-118 nt.: TTCTTATCAAGAGAAGCAGAGGGACTGGCCCGACGAAGCTTCAGCAACCGGTGTAATGGCGATCAGCCATGACCAAGGTGCTAAATCCAGCAAGCTCGAACAGCTTGGAAGATAAGAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-69 nt.: TTCTTATCTTCCAAGCTGTTCGAGCTTGCTGGATTTAGCACCTTGGTCATGGCTGATCGCCATTACACC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-69 nt.: TTCTTATCAAGAGAAGCAGAGGGACTGGCCCGACGAAGCTTCAGCAACCGGTGTAATGGCGATCAGCCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis , SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis , SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -35.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.79 kcal/mol. The frequency of the MFE structure in the ensemble is 0.57 %. The ensemble diversity is 26.23. The centroid secondary structure in dot-bracket notation with a minimum free energy of -25.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis , SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis , SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

BP5643291

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RiboSwitch type

SAM type switch

Bacteria strain target

Bordetella pertussis

Length of Switch in nucleotides

Sequence

ACATTGTTCGGCGCCGATTTGCCTGATCCGCTTGCGGGCGCCTCTTATAAATCCAGCTAAAGAGGTCTGAATGACCAATCC

Above is displayed the nucleotide sequence of the Bordetella pertussis, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 18 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 21 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 81 nt. 8) CG percentage of the sequence= 51.85% 9) *Melting temperature of the DNA based on the Wallace formula= 77.86oC 10) The entered DNA sequence(5-3) is-81 nt.: ACATTGTTCGGCGCCGATTTGCCTGATCCGCTTGCGGGCGCCTCTTATAAATCCAGCTAAAGAGGTCTGAATGACCAATCC 11) The complementary(Com) sequence(3-5) is-81 nt.: TGTAACAAGCCGCGGCTAAACGGACTAGGCGAACGCCCGCGGAGAATATTTAGGTCGATTTCTCCAGACTTACTGGTTAGG 12) The reverse(Rev) sequence(3-5) is-81 nt.: CCTAACCAGTAAGTCTGGAGAAATCGACCTAAATATTCTCCGCGGGCGTTCGCCTAGTCCGTTTAGCCGCGGCTTGTTACA 13) The RevCom sequence(5-3) is-81 nt.: GGATTGGTCATTCAGACCTCTTTAGCTGGATTTATAAGAGGCGCCCGCAAGCGGATCAGGCAAATCGGCGCCGAACAATGT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-51 nt.: ACATTGTTCGGCGCCGATTTGCCTGATCCGCTTGCGGGCGCCTCTTATAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-51 nt.: GGATTGGTCATTCAGACCTCTTTAGCTGGATTTATAAGAGGCGCCCGCAAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bordetella pertussis, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bordetella pertussis, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -20.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -21.38 kcal/mol. The frequency of the MFE structure in the ensemble is 28.26 %. The ensemble diversity is 6.59. The centroid secondary structure in dot-bracket notation with a minimum free energy of -20.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bordetella pertussis, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bordetella pertussis, SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

BA134320

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RiboSwitch type

SAM type switch

Bacteria strain target

Brucella abortis

Length of Switch in nucleotides

Sequence

CGGTAACGAACCGCGGCCTTATTTAGCGAATTCTTTAACGTGGCTGCAAGCCGGCCGGCCAAATCACCACGGAACAGGTT

Above is displayed the nucleotide sequence of the Brucella abortis , SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 16 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 80 nt. 8) CG percentage of the sequence= 55.00% 9) *Melting temperature of the DNA based on the Wallace formula= 79.05oC 10) The entered DNA sequence(5-3) is-80 nt.: CGGTAACGAACCGCGGCCTTATTTAGCGAATTCTTTAACGTGGCTGCAAGCCGGCCGGCCAAATCACCACGGAACAGGTT 11) The complementary(Com) sequence(3-5) is-80 nt.: GCCATTGCTTGGCGCCGGAATAAATCGCTTAAGAAATTGCACCGACGTTCGGCCGGCCGGTTTAGTGGTGCCTTGTCCAA 12) The reverse(Rev) sequence(3-5) is-80 nt.: TTGGACAAGGCACCACTAAACCGGCCGGCCGAACGTCGGTGCAATTTCTTAAGCGATTTATTCCGGCGCCAAGCAATGGC 13) The RevCom sequence(5-3) is-80 nt.: AACCTGTTCCGTGGTGATTTGGCCGGCCGGCTTGCAGCCACGTTAAAGAATTCGCTAAATAAGGCCGCGGTTCGTTACCG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-50 nt.: CGGTAACGAACCGCGGCCTTATTTAGCGAATTCTTTAACGTGGCTGCAAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-50 nt.: AACCTGTTCCGTGGTGATTTGGCCGGCCGGCTTGCAGCCACGTTAAAGAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Brucella abortis , SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Brucella abortis , SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -17.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.69 kcal/mol. The frequency of the MFE structure in the ensemble is 5.45 %. The ensemble diversity is 20.65. The centroid secondary structure in dot-bracket notation with a minimum free energy of -12.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Brucella abortis , SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Brucella abortis , SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

CB062450

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RiboSwitch type

SAM type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

103

Sequence

TTCTTATCAAGAGCGGTGGAGGGACTGGCCCTATGAAACCCGGCAACCAGTATATATTTTATACATGGTGCTAAATCCTGCAGATTTAACTGAAAGATGAGAA

Above is displayed the nucleotide sequence of the Clostridium botulinum , SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 19 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 27 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 103 nt. 8) CG percentage of the sequence= 41.75% 9) *Melting temperature of the DNA based on the Wallace formula= 75.49oC 10) The entered DNA sequence(5-3) is-103 nt.: TTCTTATCAAGAGCGGTGGAGGGACTGGCCCTATGAAACCCGGCAACCAGTATATATTTTATACATGGTGCTAAATCCTGCAGATTTAACTGAAAGATGAGAA 11) The complementary(Com) sequence(3-5) is-103 nt.: AAGAATAGTTCTCGCCACCTCCCTGACCGGGATACTTTGGGCCGTTGGTCATATATAAAATATGTACCACGATTTAGGACGTCTAAATTGACTTTCTACTCTT 12) The reverse(Rev) sequence(3-5) is-103 nt.: AAGAGTAGAAAGTCAATTTAGACGTCCTAAATCGTGGTACATATTTTATATATGACCAACGGCCCAAAGTATCCCGGTCAGGGAGGTGGCGAGAACTATTCTT 13) The RevCom sequence(5-3) is-103 nt.: TTCTCATCTTTCAGTTAAATCTGCAGGATTTAGCACCATGTATAAAATATATACTGGTTGCCGGGTTTCATAGGGCCAGTCCCTCCACCGCTCTTGATAAGAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: TTCTTATCAAGAGCGGTGGAGGGACTGGCCCTATGAAACCCGGCAACCAGTATATATTTTAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: TTCTCATCTTTCAGTTAAATCTGCAGGATTTAGCACCATGTATAAAATATATACTGGTTGCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum , SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum , SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -26.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -28.65 kcal/mol. The frequency of the MFE structure in the ensemble is 3.60 %. The ensemble diversity is 10.96. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum , SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum , SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

CD754670

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RiboSwitch type

SAM type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

104

Sequence

ACCTTATCAAGAGAGGCTGAGGGATAGGCCCTGTGAAGCCCAGCAACCACCCAAATGGGAAAAGGTGCTAATTCCTACAAGACAAAAGTCTTGAAAGATGAGGT

Above is displayed the nucleotide sequence of the Clostridium difficile , SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 37 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 27 nt. 4) Thiamine(T) in the sequence= 18 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 104 nt. 8) CG percentage of the sequence= 47.12% 9) *Melting temperature of the DNA based on the Wallace formula= 77.75oC 10) The entered DNA sequence(5-3) is-104 nt.: ACCTTATCAAGAGAGGCTGAGGGATAGGCCCTGTGAAGCCCAGCAACCACCCAAATGGGAAAAGGTGCTAATTCCTACAAGACAAAAGTCTTGAAAGATGAGGT 11) The complementary(Com) sequence(3-5) is-104 nt.: TGGAATAGTTCTCTCCGACTCCCTATCCGGGACACTTCGGGTCGTTGGTGGGTTTACCCTTTTCCACGATTAAGGATGTTCTGTTTTCAGAACTTTCTACTCCA 12) The reverse(Rev) sequence(3-5) is-104 nt.: TGGAGTAGAAAGTTCTGAAAACAGAACATCCTTAATCGTGGAAAAGGGTAAACCCACCAACGACCCGAAGTGTCCCGGATAGGGAGTCGGAGAGAACTATTCCA 13) The RevCom sequence(5-3) is-104 nt.: ACCTCATCTTTCAAGACTTTTGTCTTGTAGGAATTAGCACCTTTTCCCATTTGGGTGGTTGCTGGGCTTCACAGGGCCTATCCCTCAGCCTCTCTTGATAAGGT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: ACCTTATCAAGAGAGGCTGAGGGATAGGCCCTGTGAAGCCCAGCAACCACCCAAATGGGAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: ACCTCATCTTTCAAGACTTTTGTCTTGTAGGAATTAGCACCTTTTCCCATTTGGGTGGTTGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile , SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile , SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -32.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -34.34 kcal/mol. The frequency of the MFE structure in the ensemble is 9.73 %. The ensemble diversity is 19.53. The centroid secondary structure in dot-bracket notation with a minimum free energy of -25.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile , SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile , SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

CP0754004

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RiboSwitch type

SAM type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

106

Sequence

CTCTCATCTTGTAAAGAATTTCTTTACCGGAATTGGCACCGTAGTGATTTCTCACTGGTTGCCGGGTTTCATAGGGCCTTTTTCCCTCCACCTCTCTGGATAAGAG

Above is displayed the nucleotide sequence of the Clostridium perfringens , SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 22 nt. 4) Thiamine(T) in the sequence= 37 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 46.23% 9) *Melting temperature of the DNA based on the Wallace formula= 77.51oC 10) The entered DNA sequence(5-3) is-106 nt.: CTCTCATCTTGTAAAGAATTTCTTTACCGGAATTGGCACCGTAGTGATTTCTCACTGGTTGCCGGGTTTCATAGGGCCTTTTTCCCTCCACCTCTCTGGATAAGAG 11) The complementary(Com) sequence(3-5) is-106 nt.: GAGAGTAGAACATTTCTTAAAGAAATGGCCTTAACCGTGGCATCACTAAAGAGTGACCAACGGCCCAAAGTATCCCGGAAAAAGGGAGGTGGAGAGACCTATTCTC 12) The reverse(Rev) sequence(3-5) is-106 nt.: GAGAATAGGTCTCTCCACCTCCCTTTTTCCGGGATACTTTGGGCCGTTGGTCACTCTTTAGTGATGCCACGGTTAAGGCCATTTCTTTAAGAAATGTTCTACTCTC 13) The RevCom sequence(5-3) is-106 nt.: CTCTTATCCAGAGAGGTGGAGGGAAAAAGGCCCTATGAAACCCGGCAACCAGTGAGAAATCACTACGGTGCCAATTCCGGTAAAGAAATTCTTTACAAGATGAGAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: CTCTCATCTTGTAAAGAATTTCTTTACCGGAATTGGCACCGTAGTGATTTCTCACTGGTTGCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: CTCTTATCCAGAGAGGTGGAGGGAAAAAGGCCCTATGAAACCCGGCAACCAGTGAGAAATCAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens , SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens , SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -28.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -31.24 kcal/mol. The frequency of the MFE structure in the ensemble is 0.72 %. The ensemble diversity is 20.66. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens , SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium perfringens , SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

CT7800657

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RiboSwitch type

SAM type switch

Bacteria strain target

Clostridium tetani

Length of Switch in nucleotides

109

Sequence

TCCTCATCTCTCGGTTTACACCGCAGGATTTAGCACCTTATAATATGCAAACACATATACAGGTTGCCGGGCTTCATAGGGCCAGTCCCTCCACCGCTCTTAATAAGCT

Above is displayed the nucleotide sequence of the Clostridium tetani, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 33 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 30 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 109 nt. 8) CG percentage of the sequence= 47.71% 9) *Melting temperature of the DNA based on the Wallace formula= 78.29oC 10) The entered DNA sequence(5-3) is-109 nt.: TCCTCATCTCTCGGTTTACACCGCAGGATTTAGCACCTTATAATATGCAAACACATATACAGGTTGCCGGGCTTCATAGGGCCAGTCCCTCCACCGCTCTTAATAAGCT 11) The complementary(Com) sequence(3-5) is-109 nt.: AGGAGTAGAGAGCCAAATGTGGCGTCCTAAATCGTGGAATATTATACGTTTGTGTATATGTCCAACGGCCCGAAGTATCCCGGTCAGGGAGGTGGCGAGAATTATTCGA 12) The reverse(Rev) sequence(3-5) is-109 nt.: TCGAATAATTCTCGCCACCTCCCTGACCGGGATACTTCGGGCCGTTGGACATATACACAAACGTATAATATTCCACGATTTAGGACGCCACATTTGGCTCTCTACTCCT 13) The RevCom sequence(5-3) is-109 nt.: AGCTTATTAAGAGCGGTGGAGGGACTGGCCCTATGAAGCCCGGCAACCTGTATATGTGTTTGCATATTATAAGGTGCTAAATCCTGCGGTGTAAACCGAGAGATGAGGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: TCCTCATCTCTCGGTTTACACCGCAGGATTTAGCACCTTATAATATGCAAACACATATACAGGTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: AGCTTATTAAGAGCGGTGGAGGGACTGGCCCTATGAAGCCCGGCAACCTGTATATGTGTTTGCAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -21.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -24.38 kcal/mol. The frequency of the MFE structure in the ensemble is 1.79 %. The ensemble diversity is 16.80. The centroid secondary structure in dot-bracket notation with a minimum free energy of -21.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani, SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

LM430611

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RiboSwitch type

SAM type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

107

Sequence

CTCTTATCTCTCGAAGCATCACACTTCGCAGGATTTAGCACCTTTTCAACGTATTGAAAGGTTGCCGGGTTTCAACGGGCCAGTCCCTCTACCACTCATTATAAGAG

Above is displayed the nucleotide sequence of the Listeria monocytogenes , SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 26 nt. 2) Cytosine(C) in the sequence= 30 nt. 3) Guanine(G) in the sequence= 20 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 107 nt. 8) CG percentage of the sequence= 46.73% 9) *Melting temperature of the DNA based on the Wallace formula= 77.77oC 10) The entered DNA sequence(5-3) is-107 nt.: CTCTTATCTCTCGAAGCATCACACTTCGCAGGATTTAGCACCTTTTCAACGTATTGAAAGGTTGCCGGGTTTCAACGGGCCAGTCCCTCTACCACTCATTATAAGAG 11) The complementary(Com) sequence(3-5) is-107 nt.: GAGAATAGAGAGCTTCGTAGTGTGAAGCGTCCTAAATCGTGGAAAAGTTGCATAACTTTCCAACGGCCCAAAGTTGCCCGGTCAGGGAGATGGTGAGTAATATTCTC 12) The reverse(Rev) sequence(3-5) is-107 nt.: GAGAATATTACTCACCATCTCCCTGACCGGGCAACTTTGGGCCGTTGGAAAGTTATGCAACTTTTCCACGATTTAGGACGCTTCACACTACGAAGCTCTCTATTCTC 13) The RevCom sequence(5-3) is-107 nt.: CTCTTATAATGAGTGGTAGAGGGACTGGCCCGTTGAAACCCGGCAACCTTTCAATACGTTGAAAAGGTGCTAAATCCTGCGAAGTGTGATGCTTCGAGAGATAAGAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-64 nt.: CTCTTATCTCTCGAAGCATCACACTTCGCAGGATTTAGCACCTTTTCAACGTATTGAAAGGTTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-64 nt.: CTCTTATAATGAGTGGTAGAGGGACTGGCCCGTTGAAACCCGGCAACCTTTCAATACGTTGAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes , SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes , SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -24.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -26.65 kcal/mol. The frequency of the MFE structure in the ensemble is 4.99 %. The ensemble diversity is 14.31. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes , SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes , SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

NM454571

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RiboSwitch type

SAM type switch

Bacteria strain target

Neisseria meningitidis

Length of Switch in nucleotides

111

Sequence

TCAAGCGGGTTTGGATTGCTCTGGTGAGCCACATCGGCTTTTCAACCGTCCACCTTACTTTTCCTTTTGAAAAGCAGGTTGGCATGGAATTCCCAACTCTTAATGCAGCAC

Above is displayed the nucleotide sequence of the Neisseria meningitidis, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 24 nt. 2) Cytosine(C) in the sequence= 29 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 111 nt. 8) CG percentage of the sequence= 47.75% 9) *Melting temperature of the DNA based on the Wallace formula= 78.42oC 10) The entered DNA sequence(5-3) is-111 nt.: TCAAGCGGGTTTGGATTGCTCTGGTGAGCCACATCGGCTTTTCAACCGTCCACCTTACTTTTCCTTTTGAAAAGCAGGTTGGCATGGAATTCCCAACTCTTAATGCAGCAC 11) The complementary(Com) sequence(3-5) is-111 nt.: AGTTCGCCCAAACCTAACGAGACCACTCGGTGTAGCCGAAAAGTTGGCAGGTGGAATGAAAAGGAAAACTTTTCGTCCAACCGTACCTTAAGGGTTGAGAATTACGTCGTG 12) The reverse(Rev) sequence(3-5) is-111 nt.: CACGACGTAATTCTCAACCCTTAAGGTACGGTTGGACGAAAAGTTTTCCTTTTCATTCCACCTGCCAACTTTTCGGCTACACCGAGTGGTCTCGTTAGGTTTGGGCGAACT 13) The RevCom sequence(5-3) is-111 nt.: GTGCTGCATTAAGAGTTGGGAATTCCATGCCAACCTGCTTTTCAAAAGGAAAAGTAAGGTGGACGGTTGAAAAGCCGATGTGGCTCACCAGAGCAATCCAAACCCGCTTGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-66 nt.: TCAAGCGGGTTTGGATTGCTCTGGTGAGCCACATCGGCTTTTCAACCGTCCACCTTACTTTTCCTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-66 nt.: GTGCTGCATTAAGAGTTGGGAATTCCATGCCAACCTGCTTTTCAAAAGGAAAAGTAAGGTGGACGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Neisseria meningitidis, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Neisseria meningitidis, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -29.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -30.62 kcal/mol. The frequency of the MFE structure in the ensemble is 7.26 %. The ensemble diversity is 11.01. The centroid secondary structure in dot-bracket notation with a minimum free energy of -29.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Neisseria meningitidis, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Neisseria meningitidis, SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

SA14211

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RiboSwitch type

SAM type switch

Bacteria strain target

Staphylococcus aureus

Length of Switch in nucleotides

106

Sequence

CTCTCATCTTCAAAAGTTTAGACAAACTTTATGTGAATTAGCACCTTTCCAAATAGAAGGTTGCTGGGCTTCATAGGGCACATCCCTCAGCCACTCTTGATAAGAG

Above is displayed the nucleotide sequence of the Staphylococcus aureus, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 25 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 41.51% 9) *Melting temperature of the DNA based on the Wallace formula= 75.58oC 10) The entered DNA sequence(5-3) is-106 nt.: CTCTCATCTTCAAAAGTTTAGACAAACTTTATGTGAATTAGCACCTTTCCAAATAGAAGGTTGCTGGGCTTCATAGGGCACATCCCTCAGCCACTCTTGATAAGAG 11) The complementary(Com) sequence(3-5) is-106 nt.: GAGAGTAGAAGTTTTCAAATCTGTTTGAAATACACTTAATCGTGGAAAGGTTTATCTTCCAACGACCCGAAGTATCCCGTGTAGGGAGTCGGTGAGAACTATTCTC 12) The reverse(Rev) sequence(3-5) is-106 nt.: GAGAATAGTTCTCACCGACTCCCTACACGGGATACTTCGGGTCGTTGGAAGATAAACCTTTCCACGATTAAGTGTATTTCAAACAGATTTGAAAACTTCTACTCTC 13) The RevCom sequence(5-3) is-106 nt.: CTCTTATCAAGAGTGGCTGAGGGATGTGCCCTATGAAGCCCAGCAACCTTCTATTTGGAAAGGTGCTAATTCACATAAAGTTTGTCTAAACTTTTGAAGATGAGAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: CTCTCATCTTCAAAAGTTTAGACAAACTTTATGTGAATTAGCACCTTTCCAAATAGAAGGTTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: CTCTTATCAAGAGTGGCTGAGGGATGTGCCCTATGAAGCCCAGCAACCTTCTATTTGGAAAGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -25.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -27.63 kcal/mol. The frequency of the MFE structure in the ensemble is 5.13 %. The ensemble diversity is 15.85. The centroid secondary structure in dot-bracket notation with a minimum free energy of -23.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus, SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

SE001285

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RiboSwitch type

SAM type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

101

Sequence

TACTTATCATTCGAGTTGCTCGTTGGTATTAGCACCGTGCTATTTAAAGTCGGTTGCTGAAGCTTCTACGGGCCAAATCCCTCTGCTTCTCAAAATAAGGT

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 23 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 101 nt. 8) CG percentage of the sequence= 43.56% 9) *Melting temperature of the DNA based on the Wallace formula= 76.10oC 10) The entered DNA sequence(5-3) is-101 nt.: TACTTATCATTCGAGTTGCTCGTTGGTATTAGCACCGTGCTATTTAAAGTCGGTTGCTGAAGCTTCTACGGGCCAAATCCCTCTGCTTCTCAAAATAAGGT 11) The complementary(Com) sequence(3-5) is-101 nt.: ATGAATAGTAAGCTCAACGAGCAACCATAATCGTGGCACGATAAATTTCAGCCAACGACTTCGAAGATGCCCGGTTTAGGGAGACGAAGAGTTTTATTCCA 12) The reverse(Rev) sequence(3-5) is-101 nt.: TGGAATAAAACTCTTCGTCTCCCTAAACCGGGCATCTTCGAAGTCGTTGGCTGAAATTTATCGTGCCACGATTATGGTTGCTCGTTGAGCTTACTATTCAT 13) The RevCom sequence(5-3) is-101 nt.: ACCTTATTTTGAGAAGCAGAGGGATTTGGCCCGTAGAAGCTTCAGCAACCGACTTTAAATAGCACGGTGCTAATACCAACGAGCAACTCGAATGATAAGTA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: TACTTATCATTCGAGTTGCTCGTTGGTATTAGCACCGTGCTATTTAAAGTCGGTTGCTGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: ACCTTATTTTGAGAAGCAGAGGGATTTGGCCCGTAGAAGCTTCAGCAACCGACTTTAAATA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -23.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -26.35 kcal/mol. The frequency of the MFE structure in the ensemble is 1.89 %. The ensemble diversity is 16.45. The centroid secondary structure in dot-bracket notation with a minimum free energy of -18.77 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus epidermidis, SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

STS94501

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RiboSwitch type

SAM type switch

Bacteria strain target

Staphylococcus saprophyticus

Length of Switch in nucleotides

107

Sequence

CTCTTATCAAGAGTGGTGGAGGGATGTGCCCGATGAAACCCAGCAACCGTCGATTTTTCGAAATGGTGCTAAGTCACAAAAAGTTATTTAACTTTTGGAGATGAGAG

Above is displayed the nucleotide sequence of the Staphylococcus saprophyticus, SAM type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 18 nt. 3) Guanine(G) in the sequence= 28 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 107 nt. 8) CG percentage of the sequence= 42.99% 9) *Melting temperature of the DNA based on the Wallace formula= 76.24oC 10) The entered DNA sequence(5-3) is-107 nt.: CTCTTATCAAGAGTGGTGGAGGGATGTGCCCGATGAAACCCAGCAACCGTCGATTTTTCGAAATGGTGCTAAGTCACAAAAAGTTATTTAACTTTTGGAGATGAGAG 11) The complementary(Com) sequence(3-5) is-107 nt.: GAGAATAGTTCTCACCACCTCCCTACACGGGCTACTTTGGGTCGTTGGCAGCTAAAAAGCTTTACCACGATTCAGTGTTTTTCAATAAATTGAAAACCTCTACTCTC 12) The reverse(Rev) sequence(3-5) is-107 nt.: GAGAGTAGAGGTTTTCAATTTATTGAAAAACACTGAATCGTGGTAAAGCTTTTTAGCTGCCAACGACCCAAAGTAGCCCGTGTAGGGAGGTGGTGAGAACTATTCTC 13) The RevCom sequence(5-3) is-107 nt.: CTCTCATCTCCAAAAGTTAAATAACTTTTTGTGACTTAGCACCATTTCGAAAAATCGACGGTTGCTGGGTTTCATCGGGCACATCCCTCCACCACTCTTGATAAGAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-64 nt.: CTCTTATCAAGAGTGGTGGAGGGATGTGCCCGATGAAACCCAGCAACCGTCGATTTTTCGAAAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-64 nt.: CTCTCATCTCCAAAAGTTAAATAACTTTTTGTGACTTAGCACCATTTCGAAAAATCGACGGTTG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus saprophyticus, SAM type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus saprophyticus, SAM type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -27.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -29.76 kcal/mol. The frequency of the MFE structure in the ensemble is 1.13 %. The ensemble diversity is 13.07. The centroid secondary structure in dot-bracket notation with a minimum free energy of -21.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus saprophyticus, SAM type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus saprophyticus, SAM type switch.

Multiple alignment of the SAM type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the SAM type switches involved in.

Multi_resistance strains for the SAM type switches

RiboSwitch_ID:

BA647911

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RiboSwitch type

Purine type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

102

Sequence

AAATAAATAGTTAGCTACACTCATATAATCGCGGGGATATGGCCTGCAAGTTTCTACCGAAGTACCGTAAATACTTTGACTATGAGTGAGGACGAATATATT

Above is displayed the nucleotide sequence of the Bacillus anthracis , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 35 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 102 nt. 8) CG percentage of the sequence= 37.25% 9) *Melting temperature of the DNA based on the Wallace formula= 73.58oC 10) The entered DNA sequence(5-3) is-102 nt.: AAATAAATAGTTAGCTACACTCATATAATCGCGGGGATATGGCCTGCAAGTTTCTACCGAAGTACCGTAAATACTTTGACTATGAGTGAGGACGAATATATT 11) The complementary(Com) sequence(3-5) is-102 nt.: TTTATTTATCAATCGATGTGAGTATATTAGCGCCCCTATACCGGACGTTCAAAGATGGCTTCATGGCATTTATGAAACTGATACTCACTCCTGCTTATATAA 12) The reverse(Rev) sequence(3-5) is-102 nt.: TTATATAAGCAGGAGTGAGTATCAGTTTCATAAATGCCATGAAGCCATCTTTGAACGTCCGGTATAGGGGCGCTAATATACTCACATCGATTGATAAATAAA 13) The RevCom sequence(5-3) is-102 nt.: AATATATTCGTCCTCACTCATAGTCAAAGTATTTACGGTACTTCGGTAGAAACTTGCAGGCCATATCCCCGCGATTATATGAGTGTAGCTAACTATTTATTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: AAATAAATAGTTAGCTACACTCATATAATCGCGGGGATATGGCCTGCAAGTTTCTACCGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: AATATATTCGTCCTCACTCATAGTCAAAGTATTTACGGTACTTCGGTAGAAACTTGCAGGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.77 kcal/mol. The frequency of the MFE structure in the ensemble is 5.62 %. The ensemble diversity is 9.70. The centroid secondary structure in dot-bracket notation with a minimum free energy of -21.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis , Purine type switch.

Multiple alignment of the Purine type switches

Below is presented the sequences alignment of all the Purine type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Purine type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Purine riboswitches and shorter motifs based on the general one: 1) N{0,19}YTCRTATAN{0,2}YN?YRRN?RATAYGGYYYRN?RN?GTYTCTACCRRRYN{0,2}CCRTAAAN{0,2}RYYN?GACTAYGRRN?RR{0,13} 2) GTYTCTACCRRRY 3) RATAYGGYYYR Motifs identified amongst the Purine riboswitches based on the sequences alignment: 1) TDTAHG Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

The table displays known human pathogenic bacteria bearing the Purine type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BC067009

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RiboSwitch type

Purine type switch

Bacteria strain target

Bacillus cereus

Length of Switch in nucleotides

102

Sequence

AATATATTCGTCCTCACTCATAGTCAAAGTATTTACGGTACTTCGGTAGAAACTTGCAGGCCATATCCCCGCGATTATATGAGTGTAGCTAACTATTTATTT

Above is displayed the nucleotide sequence of the Bacillus cereus , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 29 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 35 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 102 nt. 8) CG percentage of the sequence= 37.25% 9) *Melting temperature of the DNA based on the Wallace formula= 73.58oC 10) The entered DNA sequence(5-3) is-102 nt.: AATATATTCGTCCTCACTCATAGTCAAAGTATTTACGGTACTTCGGTAGAAACTTGCAGGCCATATCCCCGCGATTATATGAGTGTAGCTAACTATTTATTT 11) The complementary(Com) sequence(3-5) is-102 nt.: TTATATAAGCAGGAGTGAGTATCAGTTTCATAAATGCCATGAAGCCATCTTTGAACGTCCGGTATAGGGGCGCTAATATACTCACATCGATTGATAAATAAA 12) The reverse(Rev) sequence(3-5) is-102 nt.: TTTATTTATCAATCGATGTGAGTATATTAGCGCCCCTATACCGGACGTTCAAAGATGGCTTCATGGCATTTATGAAACTGATACTCACTCCTGCTTATATAA 13) The RevCom sequence(5-3) is-102 nt.: AAATAAATAGTTAGCTACACTCATATAATCGCGGGGATATGGCCTGCAAGTTTCTACCGAAGTACCGTAAATACTTTGACTATGAGTGAGGACGAATATATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: AATATATTCGTCCTCACTCATAGTCAAAGTATTTACGGTACTTCGGTAGAAACTTGCAGGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: AAATAAATAGTTAGCTACACTCATATAATCGCGGGGATATGGCCTGCAAGTTTCTACCGAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus cereus , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus cereus , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -17.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.83 kcal/mol. The frequency of the MFE structure in the ensemble is 1.66 %. The ensemble diversity is 15.84. The centroid secondary structure in dot-bracket notation with a minimum free energy of -17.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus cereus , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus cereus , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

CB108919

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RiboSwitch type

Purine type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

102

Sequence

CACCCTAATAACATCTCCTATAGTAAAGTAGTTTAAGGCTACTCTGTAGAAACTTCTGAACCCTATTATCAGAATTATATAAGAGCGAATATTTTATTTTGT

Above is displayed the nucleotide sequence of the Clostridium botulinum , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 35 nt. 2) Cytosine(C) in the sequence= 18 nt. 3) Guanine(G) in the sequence= 13 nt. 4) Thiamine(T) in the sequence= 36 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 102 nt. 8) CG percentage of the sequence= 30.39% 9) *Melting temperature of the DNA based on the Wallace formula= 70.77oC 10) The entered DNA sequence(5-3) is-102 nt.: CACCCTAATAACATCTCCTATAGTAAAGTAGTTTAAGGCTACTCTGTAGAAACTTCTGAACCCTATTATCAGAATTATATAAGAGCGAATATTTTATTTTGT 11) The complementary(Com) sequence(3-5) is-102 nt.: GTGGGATTATTGTAGAGGATATCATTTCATCAAATTCCGATGAGACATCTTTGAAGACTTGGGATAATAGTCTTAATATATTCTCGCTTATAAAATAAAACA 12) The reverse(Rev) sequence(3-5) is-102 nt.: TGTTTTATTTTATAAGCGAGAATATATTAAGACTATTATCCCAAGTCTTCAAAGATGTCTCATCGGAATTTGATGAAATGATATCCTCTACAATAATCCCAC 13) The RevCom sequence(5-3) is-102 nt.: ACAAAATAAAATATTCGCTCTTATATAATTCTGATAATAGGGTTCAGAAGTTTCTACAGAGTAGCCTTAAACTACTTTACTATAGGAGATGTTATTAGGGTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: CACCCTAATAACATCTCCTATAGTAAAGTAGTTTAAGGCTACTCTGTAGAAACTTCTGAAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: ACAAAATAAAATATTCGCTCTTATATAATTCTGATAATAGGGTTCAGAAGTTTCTACAGAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -16.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -17.43 kcal/mol. The frequency of the MFE structure in the ensemble is 13.49 %. The ensemble diversity is 8.08. The centroid secondary structure in dot-bracket notation with a minimum free energy of -16.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

CD824001

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RiboSwitch type

Purine type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

102

Sequence

TATATAAAATATAAACTCACTCGTATATGCTCAGAAATATGGTCTGAGAGTCTCTACCAAGATACCGTAAATATCTTGACTATGAGTGAAATTATTATACCA

Above is displayed the nucleotide sequence of the Clostridium difficile , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 39 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 14 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 102 nt. 8) CG percentage of the sequence= 30.39% 9) *Melting temperature of the DNA based on the Wallace formula= 70.77oC 10) The entered DNA sequence(5-3) is-102 nt.: TATATAAAATATAAACTCACTCGTATATGCTCAGAAATATGGTCTGAGAGTCTCTACCAAGATACCGTAAATATCTTGACTATGAGTGAAATTATTATACCA 11) The complementary(Com) sequence(3-5) is-102 nt.: ATATATTTTATATTTGAGTGAGCATATACGAGTCTTTATACCAGACTCTCAGAGATGGTTCTATGGCATTTATAGAACTGATACTCACTTTAATAATATGGT 12) The reverse(Rev) sequence(3-5) is-102 nt.: ACCATATTATTAAAGTGAGTATCAGTTCTATAAATGCCATAGAACCATCTCTGAGAGTCTGGTATAAAGACTCGTATATGCTCACTCAAATATAAAATATAT 13) The RevCom sequence(5-3) is-102 nt.: TGGTATAATAATTTCACTCATAGTCAAGATATTTACGGTATCTTGGTAGAGACTCTCAGACCATATTTCTGAGCATATACGAGTGAGTTTATATTTTATATA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: TATATAAAATATAAACTCACTCGTATATGCTCAGAAATATGGTCTGAGAGTCTCTACCAAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: TGGTATAATAATTTCACTCATAGTCAAGATATTTACGGTATCTTGGTAGAGACTCTCAGAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -21.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.31 kcal/mol. The frequency of the MFE structure in the ensemble is 10.13 %. The ensemble diversity is 7.77. The centroid secondary structure in dot-bracket notation with a minimum free energy of -20.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

CP021127

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RiboSwitch type

Purine type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

100

Sequence

AAGCAAATAAGCTTTCTTCGTAATCAAGAATTCTCGGTTCTTGGTAGAGACCTCTAATCCATATCATTAGAGTTATACGAAGCAAAATTTATTTTTTTAT

Above is displayed the nucleotide sequence of the Clostridium perfringens , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 16 nt. 3) Guanine(G) in the sequence= 14 nt. 4) Thiamine(T) in the sequence= 37 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 100 nt. 8) CG percentage of the sequence= 30.00% 9) *Melting temperature of the DNA based on the Wallace formula= 70.48oC 10) The entered DNA sequence(5-3) is-100 nt.: AAGCAAATAAGCTTTCTTCGTAATCAAGAATTCTCGGTTCTTGGTAGAGACCTCTAATCCATATCATTAGAGTTATACGAAGCAAAATTTATTTTTTTAT 11) The complementary(Com) sequence(3-5) is-100 nt.: TTCGTTTATTCGAAAGAAGCATTAGTTCTTAAGAGCCAAGAACCATCTCTGGAGATTAGGTATAGTAATCTCAATATGCTTCGTTTTAAATAAAAAAATA 12) The reverse(Rev) sequence(3-5) is-100 nt.: TATTTTTTTATTTAAAACGAAGCATATTGAGATTACTATACCTAATCTCCAGAGATGGTTCTTGGCTCTTAAGAACTAATGCTTCTTTCGAATAAACGAA 13) The RevCom sequence(5-3) is-100 nt.: ATAAAAAAATAAATTTTGCTTCGTATAACTCTAATGATATGGATTAGAGGTCTCTACCAAGAACCGAGAATTCTTGATTACGAAGAAAGCTTATTTGCTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: AAGCAAATAAGCTTTCTTCGTAATCAAGAATTCTCGGTTCTTGGTAGAGACCTCTAATCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: ATAAAAAAATAAATTTTGCTTCGTATAACTCTAATGATATGGATTAGAGGTCTCTACCAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.83 kcal/mol. The frequency of the MFE structure in the ensemble is 6.03 %. The ensemble diversity is 7.45. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens , Purine type switch.

2D_Structure (A) (B)

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

CT056307

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RiboSwitch type

Purine type switch

Bacteria strain target

Clostridium tetani

Length of Switch in nucleotides

Sequence

GACAATGCTTTATTCACTCATAGTCAGAAGTTTAAGGCTTCTGGTAGATACTCCCTACCTTATTAAGGGGATATATGAGTCAATAATTTATTATAGAG

Above is displayed the nucleotide sequence of the Clostridium tetani , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 18 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 98 nt. 8) CG percentage of the sequence= 33.67% 9) *Melting temperature of the DNA based on the Wallace formula= 71.84oC 10) The entered DNA sequence(5-3) is-98 nt.: GACAATGCTTTATTCACTCATAGTCAGAAGTTTAAGGCTTCTGGTAGATACTCCCTACCTTATTAAGGGGATATATGAGTCAATAATTTATTATAGAG 11) The complementary(Com) sequence(3-5) is-98 nt.: CTGTTACGAAATAAGTGAGTATCAGTCTTCAAATTCCGAAGACCATCTATGAGGGATGGAATAATTCCCCTATATACTCAGTTATTAAATAATATCTC 12) The reverse(Rev) sequence(3-5) is-98 nt.: GAGATATTATTTAATAACTGAGTATATAGGGGAATTATTCCATCCCTCATAGATGGTCTTCGGAATTTGAAGACTGATACTCACTTATTTCGTAACAG 13) The RevCom sequence(5-3) is-98 nt.: CTCTATAATAAATTATTGACTCATATATCCCCTTAATAAGGTAGGGAGTATCTACCAGAAGCCTTAAACTTCTGACTATGAGTGAATAAAGCATTGTC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-59 nt.: GACAATGCTTTATTCACTCATAGTCAGAAGTTTAAGGCTTCTGGTAGATACTCCCTACC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-59 nt.: CTCTATAATAAATTATTGACTCATATATCCCCTTAATAAGGTAGGGAGTATCTACCAGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -24.23 kcal/mol. The frequency of the MFE structure in the ensemble is 3.69 %. The ensemble diversity is 10.93. The centroid secondary structure in dot-bracket notation with a minimum free energy of -20.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

EF961210

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RiboSwitch type

Purine type switch

Bacteria strain target

Enterococcus faecalis

Length of Switch in nucleotides

Sequence

TATCCGCTCTTCTTCACTTATAGACCAGCATTTACGGTGCTGGGTAGAGACGGTCAACCGTATTTTGACCTTATACAAGCTTCTATGTTTCTCTAGGA

Above is displayed the nucleotide sequence of the Enterococcus faecalis , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 22 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 98 nt. 8) CG percentage of the sequence= 42.86% 9) *Melting temperature of the DNA based on the Wallace formula= 75.61oC 10) The entered DNA sequence(5-3) is-98 nt.: TATCCGCTCTTCTTCACTTATAGACCAGCATTTACGGTGCTGGGTAGAGACGGTCAACCGTATTTTGACCTTATACAAGCTTCTATGTTTCTCTAGGA 11) The complementary(Com) sequence(3-5) is-98 nt.: ATAGGCGAGAAGAAGTGAATATCTGGTCGTAAATGCCACGACCCATCTCTGCCAGTTGGCATAAAACTGGAATATGTTCGAAGATACAAAGAGATCCT 12) The reverse(Rev) sequence(3-5) is-98 nt.: AGGATCTCTTTGTATCTTCGAACATATTCCAGTTTTATGCCAACTGGCAGAGATGGGTCGTGGCATTTACGACCAGATATTCACTTCTTCTCGCCTAT 13) The RevCom sequence(5-3) is-98 nt.: TCCTAGAGAAACATAGAAGCTTGTATAAGGTCAAAATACGGTTGACCGTCTCTACCCAGCACCGTAAATGCTGGTCTATAAGTGAAGAAGAGCGGATA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-59 nt.: TATCCGCTCTTCTTCACTTATAGACCAGCATTTACGGTGCTGGGTAGAGACGGTCAACC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-59 nt.: TCCTAGAGAAACATAGAAGCTTGTATAAGGTCAAAATACGGTTGACCGTCTCTACCCAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecalis , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecalis , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -24.58 kcal/mol. The frequency of the MFE structure in the ensemble is 4.04 %. The ensemble diversity is 12.00. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecalis , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecalis , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

EF610210

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RiboSwitch type

Purine type switch

Bacteria strain target

Enterococcus faecium

Length of Switch in nucleotides

Sequence

TATTAGTTTTACATACCTACTTATATATCGTCATAATATGGATGACAGTTTCTAGCCAGTACCGTAAATGCTGGACTATAAGTAAAAGATTGGCTATT

Above is displayed the nucleotide sequence of the Enterococcus faecium , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 16 nt. 4) Thiamine(T) in the sequence= 35 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 98 nt. 8) CG percentage of the sequence= 31.63% 9) *Melting temperature of the DNA based on the Wallace formula= 71.01oC 10) The entered DNA sequence(5-3) is-98 nt.: tATTAGTTTTACATACCTACTTATATATCGTCATAATATGGATGACAGTTTCTAGCCAGTACCGTAAATGCTGGACTATAAGTAAAAGATTGGCTATT 11) The complementary(Com) sequence(3-5) is-98 nt.: aTAATCAAAATGTATGGATGAATATATAGCAGTATTATACCTACTGTCAAAGATCGGTCATGGCATTTACGACCTGATATTCATTTTCTAACCGATAA 12) The reverse(Rev) sequence(3-5) is-98 nt.: TTATCGGTTAGAAAATGAATATCAGGTCGTAAATGCCATGACCGATCTTTGACAGTAGGTATAATACTGCTATATATTCATCCATACATTTTGATTAt 13) The RevCom sequence(5-3) is-98 nt.: AATAGCCAATCTTTTACTTATAGTCCAGCATTTACGGTACTGGCTAGAAACTGTCATCCATATTATGACGATATATAAGTAGGTATGTAAAACTAATa 14) The DNA sequence(5-3) to order with a 10nt overlapping region-59 nt.: tATTAGTTTTACATACCTACTTATATATCGTCATAATATGGATGACAGTTTCTAGCCAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-59 nt.: AATAGCCAATCTTTTACTTATAGTCCAGCATTTACGGTACTGGCTAGAAACTGTCATCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecium , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecium , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -15.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -17.55 kcal/mol. The frequency of the MFE structure in the ensemble is 5.89 %. The ensemble diversity is 17.73. The centroid secondary structure in dot-bracket notation with a minimum free energy of -15.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecium , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecium , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

LM41270

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RiboSwitch type

Purine type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

101

Sequence

TTCTTTATACAAACTACTCATAGTCCGGTTATTTACGGTAACCAGGTAGAAACTCGTCGCCCAATCGCAACTATTATACAAGTATTTCGGTTTTAAGTTAT

Above is displayed the nucleotide sequence of the Listeria monocytogenes , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 30 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 15 nt. 4) Thiamine(T) in the sequence= 35 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 101 nt. 8) CG percentage of the sequence= 35.64% 9) *Melting temperature of the DNA based on the Wallace formula= 72.86oC 10) The entered DNA sequence(5-3) is-101 nt.: TTCTTTATACAAACTACTCATAGTCCGGTTATTTACGGTAACCAGGTAGAAACTCGTCGCCCAATCGCAACTATTATACAAGTATTTCGGTTTTAAGTTAT 11) The complementary(Com) sequence(3-5) is-101 nt.: AAGAAATATGTTTGATGAGTATCAGGCCAATAAATGCCATTGGTCCATCTTTGAGCAGCGGGTTAGCGTTGATAATATGTTCATAAAGCCAAAATTCAATA 12) The reverse(Rev) sequence(3-5) is-101 nt.: TATTGAATTTTGGCTTTATGAACATATTATCAACGCTAACCCGCTGCTCAAAGATGGACCAATGGCATTTATTGGCCTGATACTCATCAAACATATTTCTT 13) The RevCom sequence(5-3) is-101 nt.: ATAACTTAAAACCGAAATACTTGTATAATAGTTGCGATTGGGCGACGAGTTTCTACCTGGTTACCGTAAATAACCGGACTATGAGTAGTTTGTATAAAGAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: TTCTTTATACAAACTACTCATAGTCCGGTTATTTACGGTAACCAGGTAGAAACTCGTCGCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: ATAACTTAAAACCGAAATACTTGTATAATAGTTGCGATTGGGCGACGAGTTTCTACCTGGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -11.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -13.18 kcal/mol. The frequency of the MFE structure in the ensemble is 9.03 %. The ensemble diversity is 27.50. The centroid secondary structure in dot-bracket notation with a minimum free energy of -7.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

SA436006

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RiboSwitch type

Purine type switch

Bacteria strain target

Staphylococcus aureus

Length of Switch in nucleotides

103

Sequence

CAGTGTTATTCATTTACTCATAGTCGTGTCGTTTAAGGCAACACGGTAGAAACTTCCAAAGCCATATTCTTCAGATTATATGAGTTTTTAGTAATAAATTATT

Above is displayed the nucleotide sequence of the Staphylococcus aureus , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 16 nt. 3) Guanine(G) in the sequence= 16 nt. 4) Thiamine(T) in the sequence= 39 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 103 nt. 8) CG percentage of the sequence= 31.07% 9) *Melting temperature of the DNA based on the Wallace formula= 71.11oC 10) The entered DNA sequence(5-3) is-103 nt.: CAGTGTTATTCATTTACTCATAGTCGTGTCGTTTAAGGCAACACGGTAGAAACTTCCAAAGCCATATTCTTCAGATTATATGAGTTTTTAGTAATAAATTATT 11) The complementary(Com) sequence(3-5) is-103 nt.: GTCACAATAAGTAAATGAGTATCAGCACAGCAAATTCCGTTGTGCCATCTTTGAAGGTTTCGGTATAAGAAGTCTAATATACTCAAAAATCATTATTTAATAA 12) The reverse(Rev) sequence(3-5) is-103 nt.: TTATTAAATAATGATTTTTGAGTATATTAGACTTCTTATACCGAAACCTTCAAAGATGGCACAACGGAATTTGCTGTGCTGATACTCATTTACTTATTGTGAC 13) The RevCom sequence(5-3) is-103 nt.: AATAATTTATTACTAAAAACTCATATAATCTGAAGAATATGGCTTTGGAAGTTTCTACCGTGTTGCCTTAAACGACACGACTATGAGTAAATGAATAACACTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: CAGTGTTATTCATTTACTCATAGTCGTGTCGTTTAAGGCAACACGGTAGAAACTTCCAAAGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: AATAATTTATTACTAAAAACTCATATAATCTGAAGAATATGGCTTTGGAAGTTTCTACCGTG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -14.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -17.20 kcal/mol. The frequency of the MFE structure in the ensemble is 2.03 %. The ensemble diversity is 18.36. The centroid secondary structure in dot-bracket notation with a minimum free energy of -13.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

SE456210

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RiboSwitch type

Purine type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

Sequence

CATAAAATAATTTATATGACTCATATAATCTAGAGAATATGGCTTTAGAAGTTTCTACCGTGTCGCCATAAACGACACGACTATGAGTAACAATCCAATACAT

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis, Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 24 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 11 nt. 4) Thiamine(T) in the sequence= 18 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 68 nt. 8) CG percentage of the sequence= 38.24% 9) *Melting temperature of the DNA based on the Wallace formula= 70.69oC 10) The entered DNA sequence(5-3) is-68 nt.: AATATGGCTTTAGAAGTTTCTACCGTGTCGCCATAAACGACACGACTATGAGTAACAATCCAATACAT 11) The complementary(Com) sequence(3-5) is-68 nt.: TTATACCGAAATCTTCAAAGATGGCACAGCGGTATTTGCTGTGCTGATACTCATTGTTAGGTTATGTA 12) The reverse(Rev) sequence(3-5) is-68 nt.: TACATAACCTAACAATGAGTATCAGCACAGCAAATACCGCTGTGCCATCTTTGAAGATTTCGGTATAA 13) The RevCom sequence(5-3) is-68 nt.: ATGTATTGGATTGTTACTCATAGTCGTGTCGTTTATGGCGACACGGTAGAAACTTCTAAAGCCATATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-44 nt.: AATATGGCTTTAGAAGTTTCTACCGTGTCGCCATAAACGACACG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-44 nt.: ATGTATTGGATTGTTACTCATAGTCGTGTCGTTTATGGCGACAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis, Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis, Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -21.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -22.61 kcal/mol. The frequency of the MFE structure in the ensemble is 14.15 %. The ensemble diversity is 7.03. The centroid secondary structure in dot-bracket notation with a minimum free energy of -20.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis, Purine type switch.

2D_Structure (A) (B)

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

StS19830

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RiboSwitch type

Purine type switch

Bacteria strain target

Staphylococcus saprophyticus

Length of Switch in nucleotides

103

Sequence

TGTATTGTATTGGTTACTCATAGTCATGTTGTTAATGGCAACATGGTAGAAACTTCTAAAGCCGTATCCTTCAGATTATATGAGTTAGATAAATTATTAACTG

Above is displayed the nucleotide sequence of the Staphylococcus saprophyticus, Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 13 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 39 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 103 nt. 8) CG percentage of the sequence= 31.07% 9) *Melting temperature of the DNA based on the Wallace formula= 71.11oC 10) The entered DNA sequence(5-3) is-103 nt.: TGTATTGTATTGGTTACTCATAGTCATGTTGTTAATGGCAACATGGTAGAAACTTCTAAAGCCGTATCCTTCAGATTATATGAGTTAGATAAATTATTAACTG 11) The complementary(Com) sequence(3-5) is-103 nt.: ACATAACATAACCAATGAGTATCAGTACAACAATTACCGTTGTACCATCTTTGAAGATTTCGGCATAGGAAGTCTAATATACTCAATCTATTTAATAATTGAC 12) The reverse(Rev) sequence(3-5) is-103 nt.: GTCAATTATTAAATAGATTGAGTATATTAGACTTCCTATGCCGAAATCTTCAAAGATGGTACAACGGTAATTGTTGTACTGATACTCATTGGTTATGTTATGT 13) The RevCom sequence(5-3) is-103 nt.: CAGTTAATAATTTATCTAACTCATATAATCTGAAGGATACGGCTTTAGAAGTTTCTACCATGTTGCCATTAACAACATGACTATGAGTAACCAATACAATACA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: TGTATTGTATTGGTTACTCATAGTCATGTTGTTAATGGCAACATGGTAGAAACTTCTAAAGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: CAGTTAATAATTTATCTAACTCATATAATCTGAAGGATACGGCTTTAGAAGTTTCTACCATG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus saprophyticus, Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus saprophyticus, Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -16.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.29 kcal/mol. The frequency of the MFE structure in the ensemble is 1.08 %. The ensemble diversity is 24.28. The centroid secondary structure in dot-bracket notation with a minimum free energy of -14.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus saprophyticus, Purine type switch.

2D_Structure (A) (B)

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

SA0864121

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RiboSwitch type

Purine type switch

Bacteria strain target

Streptococcus agalactiae

Length of Switch in nucleotides

Sequence

GCTATTTATTAGCTTACTTATTGTTAGACATTACGGTGTCTTGTAGAGACGCTAAGCCAATCCTCAGCATAAATAAGTAAATCATATATTTAATTG

Above is displayed the nucleotide sequence of the Streptococcus agalactiae, Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 15 nt. 4) Thiamine(T) in the sequence= 35 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 96 nt. 8) CG percentage of the sequence= 31.25% 9) *Melting temperature of the DNA based on the Wallace formula= 70.71oC 10) The entered DNA sequence(5-3) is-96 nt.: GCTATTTATTAGCTTACTTATTGTTAGACATTACGGTGTCTTGTAGAGACGCTAAGCCAATCCTCAGCATAAATAAGTAAATCATATATTTAATTG 11) The complementary(Com) sequence(3-5) is-96 nt.: CGATAAATAATCGAATGAATAACAATCTGTAATGCCACAGAACATCTCTGCGATTCGGTTAGGAGTCGTATTTATTCATTTAGTATATAAATTAAC 12) The reverse(Rev) sequence(3-5) is-96 nt.: GTTAATTTATATACTAAATGAATAAATACGACTCCTAACCGAATCGCAGAGATGTTCTGTGGCATTACAGATTGTTATTCATTCGATTATTTATCG 13) The RevCom sequence(5-3) is-96 nt.: CAATTAAATATATGATTTACTTATTTATGCTGAGGATTGGCTTAGCGTCTCTACAAGACACCGTAATGTCTAACAATAAGTAAGCTAATAAATAGC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-58 nt.: GCTATTTATTAGCTTACTTATTGTTAGACATTACGGTGTCTTGTAGAGACGCTAAGCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-58 nt.: CAATTAAATATATGATTTACTTATTTATGCTGAGGATTGGCTTAGCGTCTCTACAAGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus agalactiae, Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus agalactiae, Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -17.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.13 kcal/mol. The frequency of the MFE structure in the ensemble is 8.33 %. The ensemble diversity is 9.86. The centroid secondary structure in dot-bracket notation with a minimum free energy of -16.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus agalactiae, Purine type switch.

2D_Structure (A) (B)

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

SP129811

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RiboSwitch type

Purine type switch

Bacteria strain target

Streptococcus pneumoniae

Length of Switch in nucleotides

Sequence

AAAATTGAATATCGTTTTACTTGTTTATGTCGTGAATTGGCACGACGTTTCTACAAGGTGCCGGAACACCTAACAATAAGTAAGTCAGCAGTGAGA

Above is displayed the nucleotide sequence of the Streptococcus pneumoniae , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 16 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 28 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 96 nt. 8) CG percentage of the sequence= 38.54% 9) *Melting temperature of the DNA based on the Wallace formula= 73.70oC 10) The entered DNA sequence(5-3) is-96 nt.: AAAATTGAATATCGTTTTACTTGTTTATGTCGTGAATTGGCACGACGTTTCTACAAGGTGCCGGAACACCTAACAATAAGTAAGTCAGCAGTGAGA 11) The complementary(Com) sequence(3-5) is-96 nt.: TTTTAACTTATAGCAAAATGAACAAATACAGCACTTAACCGTGCTGCAAAGATGTTCCACGGCCTTGTGGATTGTTATTCATTCAGTCGTCACTCT 12) The reverse(Rev) sequence(3-5) is-96 nt.: AGAGTGACGACTGAATGAATAACAATCCACAAGGCCGTGGAACATCTTTGCAGCACGGTTAAGTGCTGTATTTGTTCATTTTGCTATAAGTTAAAA 13) The RevCom sequence(5-3) is-96 nt.: TCTCACTGCTGACTTACTTATTGTTAGGTGTTCCGGCACCTTGTAGAAACGTCGTGCCAATTCACGACATAAACAAGTAAAACGATATTCAATTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-58 nt.: AAAATTGAATATCGTTTTACTTGTTTATGTCGTGAATTGGCACGACGTTTCTACAAGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-58 nt.: TCTCACTGCTGACTTACTTATTGTTAGGTGTTCCGGCACCTTGTAGAAACGTCGTGCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus pneumoniae , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus pneumoniae , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -21.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -22.89 kcal/mol. The frequency of the MFE structure in the ensemble is 5.48 %. The ensemble diversity is 12.80 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -20.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus pneumoniae , Purine type switch.

2D_Structure (A) (B)

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

SP481311

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RiboSwitch type

Purine type switch

Bacteria strain target

Streptococcus pyogenes

Length of Switch in nucleotides

Sequence

TGAATTCAATAATGACATACTTATTTATGCTGTGAATTGGCGCAGCGTCTCTACAAGACACCTTAATGTCTAACAATAAGTAAGCTTTTAGGCTTG

Above is displayed the nucleotide sequence of the Streptococcus pyogenes , Purine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 30 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 96 nt. 8) CG percentage of the sequence= 35.42% 9) *Melting temperature of the DNA based on the Wallace formula= 72.42oC 10) The entered DNA sequence(5-3) is-96 nt.: TGAATTCAATAATGACATACTTATTTATGCTGTGAATTGGCGCAGCGTCTCTACAAGACACCTTAATGTCTAACAATAAGTAAGCTTTTAGGCTTG 11) The complementary(Com) sequence(3-5) is-96 nt.: ACTTAAGTTATTACTGTATGAATAAATACGACACTTAACCGCGTCGCAGAGATGTTCTGTGGAATTACAGATTGTTATTCATTCGAAAATCCGAAC 12) The reverse(Rev) sequence(3-5) is-96 nt.: GTTCGGATTTTCGAATGAATAACAATCTGTAATTCCACAGAACATCTCTGCGACGCGGTTAAGTGTCGTATTTATTCATACAGTAATAACTTAAGT 13) The RevCom sequence(5-3) is-96 nt.: CAAGCCTAAAAGCTTACTTATTGTTAGACATTAAGGTGTCTTGTAGAGACGCTGCGCCAATTCACAGCATAAATAAGTATGTCATTATTGAATTCA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-58 nt.: TGAATTCAATAATGACATACTTATTTATGCTGTGAATTGGCGCAGCGTCTCTACAAGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-58 nt.: CAAGCCTAAAAGCTTACTTATTGTTAGACATTAAGGTGTCTTGTAGAGACGCTGCGCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus pyogenes , Purine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus pyogenes , Purine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -20.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -21.69 kcal/mol. The frequency of the MFE structure in the ensemble is 8.84 %. The ensemble diversity is 7.09. The centroid secondary structure in dot-bracket notation with a minimum free energy of -20.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus pyogenes , Purine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus pyogenes , Purine type switch.

Multiple alignment of the Purine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Purine type switches involved in.

Multi_resistance strains for the Purine type switches

RiboSwitch_ID:

BA44011

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RiboSwitch type

TPP type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

106

Sequence

TTTATCCACTAGGGGGGCCTATTATAGGCTGAGATCAAATTGGAATTTGAGACTCTTAGTACCTGATCTGGTTAATGCCAGCGTAGGGAAGTGGGAAAGACATTGC

Above is displayed the nucleotide sequence of the Bacillus anthracis , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 29 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 30 nt. 4) Thiamine(T) in the sequence= 30 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 44.34% 9) *Melting temperature of the DNA based on the Wallace formula= 76.74oC 10) The entered DNA sequence(5-3) is-106 nt.: TTTATCCACTAGGGGGGCCTATTATAGGCTGAGATCAAATTGGAATTTGAGACTCTTAGTACCTGATCTGGTTAATGCCAGCGTAGGGAAGTGGGAAAGACATTGC 11) The complementary(Com) sequence(3-5) is-106 nt.: AAATAGGTGATCCCCCCGGATAATATCCGACTCTAGTTTAACCTTAAACTCTGAGAATCATGGACTAGACCAATTACGGTCGCATCCCTTCACCCTTTCTGTAACG 12) The reverse(Rev) sequence(3-5) is-106 nt.: CGTTACAGAAAGGGTGAAGGGATGCGACCGTAATTGGTCTAGTCCATGATTCTCAGAGTTTAAGGTTAAACTAGAGTCGGATATTATCCGGGGGGATCACCTATTT 13) The RevCom sequence(5-3) is-106 nt.: GCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGATCAGGTACTAAGAGTCTCAAATTCCAATTTGATCTCAGCCTATAATAGGCCCCCCTAGTGGATAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: TTTATCCACTAGGGGGGCCTATTATAGGCTGAGATCAAATTGGAATTTGAGACTCTTAGTACC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: GCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGATCAGGTACTAAGAGTCTCAAATT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -29.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -31.34 kcal/mol. The frequency of the MFE structure in the ensemble is 3.63 %. The ensemble diversity is 17.36. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis , TPP type switch.

Multiple alignment of the TPP type switches

Below is presented the sequences alignment of all the TPP type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the TPP type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the TPP riboswitches and shorter motifs based on the general one: 1) N{0,6}YN{0,4}GGGGN?GCYN{0,9}RGCTGAGAN{0,13}RACCCN?YN?RRACCTGATCYRGN?TN?ATRCYRGCGN?AGGGAN{0,3}RN{0,13} 2) RRACCTGATCYRG Motifs identified amongst the TPP riboswitches based on the sequences alignment: 1) TCTCAGC 2) TGCCAGC 3) TACCAGC Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

The table displays known human pathogenic bacteria bearing the TPP type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BC43281

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RiboSwitch type

TPP type switch

Bacteria strain target

Bacillus cereus

Length of Switch in nucleotides

106

Sequence

ATAATCGTCTTCCCACTTCCCTACGCTGGTATTAACCAGATCAGGTACTAAGAGTCTCAAAATTATGTTTGATCTCAGCCTACAAAAGGCCCCCCTAGTGGATAAA

Above is displayed the nucleotide sequence of the Bacillus cereus, TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 28 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 42.45% 9) *Melting temperature of the DNA based on the Wallace formula= 75.96oC 10) The entered DNA sequence(5-3) is-106 nt.: ATAATCGTCTTCCCACTTCCCTACGCTGGTATTAACCAGATCAGGTACTAAGAGTCTCAAAATTATGTTTGATCTCAGCCTACAAAAGGCCCCCCTAGTGGATAAA 11) The complementary(Com) sequence(3-5) is-106 nt.: TATTAGCAGAAGGGTGAAGGGATGCGACCATAATTGGTCTAGTCCATGATTCTCAGAGTTTTAATACAAACTAGAGTCGGATGTTTTCCGGGGGGATCACCTATTT 12) The reverse(Rev) sequence(3-5) is-106 nt.: AAATAGGTGATCCCCCCGGAAAACATCCGACTCTAGTTTGTATTAAAACTCTGAGAATCATGGACTAGACCAATTATGGTCGCATCCCTTCACCCTTCTGCTAATA 13) The RevCom sequence(5-3) is-106 nt.: TTTATCCACTAGGGGGGCCTTTTGTAGGCTGAGATCAAACATAATTTTGAGACTCTTAGTACCTGATCTGGTTAATACCAGCGTAGGGAAGTGGGAAGACGATTAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: ATAATCGTCTTCCCACTTCCCTACGCTGGTATTAACCAGATCAGGTACTAAGAGTCTCAAAAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: TTTATCCACTAGGGGGGCCTTTTGTAGGCTGAGATCAAACATAATTTTGAGACTCTTAGTACC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus cereus, TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus cereus, TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -24.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -24.70 kcal/mol. The frequency of the MFE structure in the ensemble is 44.36 %. The ensemble diversity is 2.25. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus cereus, TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus cereus, TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

BS10912

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RiboSwitch type

TPP type switch

Bacteria strain target

Bacillus subtilis

Length of Switch in nucleotides

109

Sequence

TTTAACCACTAGGGGTGTCCTTCATAAGGGCTGAGATAAAAGTGTGACTTTTAGACCCTCATAACTTGAACAGGTTCAGACCTGCGTAGGGAAGTGGAGCGGTATTTGT

Above is displayed the nucleotide sequence of the Bacillus subtilis, TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 29 nt. 2) Cytosine(C) in the sequence= 19 nt. 3) Guanine(G) in the sequence= 30 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 109 nt. 8) CG percentage of the sequence= 44.95% 9) *Melting temperature of the DNA based on the Wallace formula= 77.16oC 10) The entered DNA sequence(5-3) is-109 nt.: TTTAACCACTAGGGGTGTCCTTCATAAGGGCTGAGATAAAAGTGTGACTTTTAGACCCTCATAACTTGAACAGGTTCAGACCTGCGTAGGGAAGTGGAGCGGTATTTGT 11) The complementary(Com) sequence(3-5) is-109 nt.: AAATTGGTGATCCCCACAGGAAGTATTCCCGACTCTATTTTCACACTGAAAATCTGGGAGTATTGAACTTGTCCAAGTCTGGACGCATCCCTTCACCTCGCCATAAACA 12) The reverse(Rev) sequence(3-5) is-109 nt.: TGTTTATGGCGAGGTGAAGGGATGCGTCCAGACTTGGACAAGTTCAATACTCCCAGATTTTCAGTGTGAAAATAGAGTCGGGAATACTTCCTGTGGGGATCACCAATTT 13) The RevCom sequence(5-3) is-109 nt.: ACAAATACCGCTCCACTTCCCTACGCAGGTCTGAACCTGTTCAAGTTATGAGGGTCTAAAAGTCACACTTTTATCTCAGCCCTTATGAAGGACACCCCTAGTGGTTAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: TTTAACCACTAGGGGTGTCCTTCATAAGGGCTGAGATAAAAGTGTGACTTTTAGACCCTCATAAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: ACAAATACCGCTCCACTTCCCTACGCAGGTCTGAACCTGTTCAAGTTATGAGGGTCTAAAAGTCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus subtilis, TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus subtilis, TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -26.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -27.42 kcal/mol. The frequency of the MFE structure in the ensemble is 9.95 %. The ensemble diversity is 16.83. The centroid secondary structure in dot-bracket notation with a minimum free energy of -26.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus subtilis, TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus subtilis, TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

BP611201

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RiboSwitch type

TPP type switch

Bacteria strain target

Bordetella pertussis

Length of Switch in nucleotides

112

Sequence

AGGATCACGCAGGGGTACTCGCTGTCCCGCCTTCAAGGCCGGCAGCGTGTTGAGAGAGTCCCTTCGTACCAGTACGGATAATGCCGATGCTGGGAGCGTATTCCAGTTGCCG

Above is displayed the nucleotide sequence of the Bordetella pertussis, TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 21 nt. 2) Cytosine(C) in the sequence= 31 nt. 3) Guanine(G) in the sequence= 36 nt. 4) Thiamine(T) in the sequence= 24 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 112 nt. 8) CG percentage of the sequence= 59.82% 9) *Melting temperature of the DNA based on the Wallace formula= 83.42oC 10) The entered DNA sequence(5-3) is-112 nt.: AGGATCACGCAGGGGTACTCGCTGTCCCGCCTTCAAGGCCGGCAGCGTGTTGAGAGAGTCCCTTCGTACCAGTACGGATAATGCCGATGCTGGGAGCGTATTCCAGTTGCCG 11) The complementary(Com) sequence(3-5) is-112 nt.: TCCTAGTGCGTCCCCATGAGCGACAGGGCGGAAGTTCCGGCCGTCGCACAACTCTCTCAGGGAAGCATGGTCATGCCTATTACGGCTACGACCCTCGCATAAGGTCAACGGC 12) The reverse(Rev) sequence(3-5) is-112 nt.: GCCGTTGACCTTATGCGAGGGTCGTAGCCGTAATAGGCATGACCATGCTTCCCTGAGAGAGTTGTGCGACGGCCGGAACTTCCGCCCTGTCGCTCATGGGGACGCACTAGGA 13) The RevCom sequence(5-3) is-112 nt.: CGGCAACTGGAATACGCTCCCAGCATCGGCATTATCCGTACTGGTACGAAGGGACTCTCTCAACACGCTGCCGGCCTTGAAGGCGGGACAGCGAGTACCCCTGCGTGATCCT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-66 nt.: AGGATCACGCAGGGGTACTCGCTGTCCCGCCTTCAAGGCCGGCAGCGTGTTGAGAGAGTCCCTTCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-66 nt.: CGGCAACTGGAATACGCTCCCAGCATCGGCATTATCCGTACTGGTACGAAGGGACTCTCTCAACAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bordetella pertussis, TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bordetella pertussis, TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -43.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -44.82 kcal/mol. The frequency of the MFE structure in the ensemble is 19.13 %. The ensemble diversity is 7.86. The centroid secondary structure in dot-bracket notation with a minimum free energy of -43.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bordetella pertussis, TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bordetella pertussis, TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

BA00135

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RiboSwitch type

TPP type switch

Bacteria strain target

Brucella abortus

Length of Switch in nucleotides

107

Sequence

GACGCGCCAAACTCCGTTCCCTACGCAGGTATTACCCGGATCAGGTTCAATGGGTTGACGCGAGAATGCGTCTCTCAGCCTCTTTCAAGGCACCCCAACGAATTTTG

Above is displayed the nucleotide sequence of the Brucella abortus, TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 24 nt. 2) Cytosine(C) in the sequence= 33 nt. 3) Guanine(G) in the sequence= 25 nt. 4) Thiamine(T) in the sequence= 25 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 107 nt. 8) CG percentage of the sequence= 54.21% 9) *Melting temperature of the DNA based on the Wallace formula= 80.84oC 10) The entered DNA sequence(5-3) is-107 nt.: GACGCGCCAAACTCCGTTCCCTACGCAGGTATTACCCGGATCAGGTTCAATGGGTTGACGCGAGAATGCGTCTCTCAGCCTCTTTCAAGGCACCCCAACGAATTTTG 11) The complementary(Com) sequence(3-5) is-107 nt.: CTGCGCGGTTTGAGGCAAGGGATGCGTCCATAATGGGCCTAGTCCAAGTTACCCAACTGCGCTCTTACGCAGAGAGTCGGAGAAAGTTCCGTGGGGTTGCTTAAAAC 12) The reverse(Rev) sequence(3-5) is-107 nt.: GTTTTAAGCAACCCCACGGAACTTTCTCCGACTCTCTGCGTAAGAGCGCAGTTGGGTAACTTGGACTAGGCCCATTATGGACGCATCCCTTGCCTCAAACCGCGCAG 13) The RevCom sequence(5-3) is-107 nt.: CAAAATTCGTTGGGGTGCCTTGAAAGAGGCTGAGAGACGCATTCTCGCGTCAACCCATTGAACCTGATCCGGGTAATACCTGCGTAGGGAACGGAGTTTGGCGCGTC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-64 nt.: GACGCGCCAAACTCCGTTCCCTACGCAGGTATTACCCGGATCAGGTTCAATGGGTTGACGCGAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-64 nt.: CAAAATTCGTTGGGGTGCCTTGAAAGAGGCTGAGAGACGCATTCTCGCGTCAACCCATTGAACC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Brucella abortus, TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Brucella abortus, TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -24.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -26.68 kcal/mol. The frequency of the MFE structure in the ensemble is 5.55 %. The ensemble diversity is 28.36. The centroid secondary structure in dot-bracket notation with a minimum free energy of -18.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Brucella abortus, TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Brucella abortus, TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

CJ010455

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RiboSwitch type

TPP type switch

Bacteria strain target

Campylobacter jejuni

Length of Switch in nucleotides

105

Sequence

AACATAAATGACGGGAGCTTGTGTAACAGGCTGAGAGTAAGCTAAAAGCTTAGACCGAACCGGATCTGGATAATACCAGCGTCGGGAAGATTTATAAATTTCAAT

Above is displayed the nucleotide sequence of the Campylobacter jejuni, TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 38 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 26 nt. 4) Thiamine(T) in the sequence= 24 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 105 nt. 8) CG percentage of the sequence= 40.95% 9) *Melting temperature of the DNA based on the Wallace formula= 75.29oC 10) The entered DNA sequence(5-3) is-105 nt.: AACATAAATGACGGGAGCTTGTGTAACAGGCTGAGAGTAAGCTAAAAGCTTAGACCGAACCGGATCTGGATAATACCAGCGTCGGGAAGATTTATAAATTTCAAT 11) The complementary(Com) sequence(3-5) is-105 nt.: TTGTATTTACTGCCCTCGAACACATTGTCCGACTCTCATTCGATTTTCGAATCTGGCTTGGCCTAGACCTATTATGGTCGCAGCCCTTCTAAATATTTAAAGTTA 12) The reverse(Rev) sequence(3-5) is-105 nt.: TAACTTTAAATATTTAGAAGGGCTGCGACCATAATAGGTCTAGGCCAAGCCAGATTCGAAAATCGAATGAGAGTCGGACAATGTGTTCGAGGGCAGTAAATACAA 13) The RevCom sequence(5-3) is-105 nt.: ATTGAAATTTATAAATCTTCCCGACGCTGGTATTATCCAGATCCGGTTCGGTCTAAGCTTTTAGCTTACTCTCAGCCTGTTACACAAGCTCCCGTCATTTATGTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: AACATAAATGACGGGAGCTTGTGTAACAGGCTGAGAGTAAGCTAAAAGCTTAGACCGAACCGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: ATTGAAATTTATAAATCTTCCCGACGCTGGTATTATCCAGATCCGGTTCGGTCTAAGCTTTTA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Campylobacter jejuni, TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Campylobacter jejuni, TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -23.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -25.20 kcal/mol. The frequency of the MFE structure in the ensemble is 10.25 %. The ensemble diversity is 12.75. The centroid secondary structure in dot-bracket notation with a minimum free energy of -18.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Campylobacter jejuni, TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Campylobacter jejuni, TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

CB05521

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RiboSwitch type

TPP type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

106

Sequence

ATTAAGTGCTAGGGGTGCCAAAAGTTATGGCTGAGAAATGATAAATTCATTAACCCTCTAACCTGATCTGGTTAATACCAGCGTAGGAAAGCTTGAGTGTTAATAA

Above is displayed the nucleotide sequence of the Clostridium botulinum , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 16 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 30 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 37.74% 9) *Melting temperature of the DNA based on the Wallace formula= 74.03oC 10) The entered DNA sequence(5-3) is-106 nt.: ATTAAGTGCTAGGGGTGCCAAAAGTTATGGCTGAGAAATGATAAATTCATTAACCCTCTAACCTGATCTGGTTAATACCAGCGTAGGAAAGCTTGAGTGTTAATAA 11) The complementary(Com) sequence(3-5) is-106 nt.: TAATTCACGATCCCCACGGTTTTCAATACCGACTCTTTACTATTTAAGTAATTGGGAGATTGGACTAGACCAATTATGGTCGCATCCTTTCGAACTCACAATTATT 12) The reverse(Rev) sequence(3-5) is-106 nt.: AATAATTGTGAGTTCGAAAGGATGCGACCATAATTGGTCTAGTCCAATCTCCCAATTACTTAAATAGTAAAGAGTCGGTATTGAAAACCGTGGGGATCGTGAATTA 13) The RevCom sequence(5-3) is-106 nt.: TTATTAACACTCAAGCTTTCCTACGCTGGTATTAACCAGATCAGGTTAGAGGGTTAATGAATTTATCATTTCTCAGCCATAACTTTTGGCACCCCTAGCACTTAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: ATTAAGTGCTAGGGGTGCCAAAAGTTATGGCTGAGAAATGATAAATTCATTAACCCTCTAACC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: TTATTAACACTCAAGCTTTCCTACGCTGGTATTAACCAGATCAGGTTAGAGGGTTAATGAATT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -24.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -25.87 kcal/mol. The frequency of the MFE structure in the ensemble is 12.68 %. The ensemble diversity is 18.61. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

CD043121

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RiboSwitch type

TPP type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

112

Sequence

AATTAGAGCTAGGGGCGCTAGAATTGGCTAGCTGAGAGATAAAGCCGTAACTTACAAACCCTAATAACCTGATCAAGATAATGCTTGCGAAGGGAAGCTTTTTAATATAATT

Above is displayed the nucleotide sequence of the Clostridium difficile , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 40 nt. 2) Cytosine(C) in the sequence= 18 nt. 3) Guanine(G) in the sequence= 25 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 112 nt. 8) CG percentage of the sequence= 38.39% 9) *Melting temperature of the DNA based on the Wallace formula= 74.64oC 10) The entered DNA sequence(5-3) is-112 nt.: AATTAGAGCTAGGGGCGCTAGAATTGGCTAGCTGAGAGATAAAGCCGTAACTTACAAACCCTAATAACCTGATCAAGATAATGCTTGCGAAGGGAAGCTTTTTAATATAATT 11) The complementary(Com) sequence(3-5) is-112 nt.: TTAATCTCGATCCCCGCGATCTTAACCGATCGACTCTCTATTTCGGCATTGAATGTTTGGGATTATTGGACTAGTTCTATTACGAACGCTTCCCTTCGAAAAATTATATTAA 12) The reverse(Rev) sequence(3-5) is-112 nt.: TTAATATAATTTTTCGAAGGGAAGCGTTCGTAATAGAACTAGTCCAATAATCCCAAACATTCAATGCCGAAATAGAGAGTCGATCGGTTAAGATCGCGGGGATCGAGATTAA 13) The RevCom sequence(5-3) is-112 nt.: AATTATATTAAAAAGCTTCCCTTCGCAAGCATTATCTTGATCAGGTTATTAGGGTTTGTAAGTTACGGCTTTATCTCTCAGCTAGCCAATTCTAGCGCCCCTAGCTCTAATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-66 nt.: AATTAGAGCTAGGGGCGCTAGAATTGGCTAGCTGAGAGATAAAGCCGTAACTTACAAACCCTAATA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-66 nt.: AATTATATTAAAAAGCTTCCCTTCGCAAGCATTATCTTGATCAGGTTATTAGGGTTTGTAAGTTAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -20.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -22.52 kcal/mol. The frequency of the MFE structure in the ensemble is 2.74 %. The ensemble diversity is 18.52. The centroid secondary structure in dot-bracket notation with a minimum free energy of -19.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

CP011221

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RiboSwitch type

TPP type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

103

Sequence

AAAACTTTCTACAGGCTTTCCTACGCTGGTATTATCCAGATCAGGTTTTAAGGGTTAATAACGAAATGTTATCTCTCAGCCAAAGGCACCCCTAGCTATAAAG

Above is displayed the nucleotide sequence of the Clostridium perfringens , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 23 nt. 3) Guanine(G) in the sequence= 18 nt. 4) Thiamine(T) in the sequence= 30 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 103 nt. 8) CG percentage of the sequence= 39.81% 9) *Melting temperature of the DNA based on the Wallace formula= 74.69oC 10) The entered DNA sequence(5-3) is-103 nt.: AAAACTTTCTACAGGCTTTCCTACGCTGGTATTATCCAGATCAGGTTTTAAGGGTTAATAACGAAATGTTATCTCTCAGCCAAAGGCACCCCTAGCTATAAAG 11) The complementary(Com) sequence(3-5) is-103 nt.: TTTTGAAAGATGTCCGAAAGGATGCGACCATAATAGGTCTAGTCCAAAATTCCCAATTATTGCTTTACAATAGAGAGTCGGTTTCCGTGGGGATCGATATTTC 12) The reverse(Rev) sequence(3-5) is-103 nt.: GAAATATCGATCCCCACGGAAACCGACTCTCTATTGTAAAGCAATAATTGGGAATTTTGGACTAGACCTATTATGGTCGCATCCTTTCGGACATCTTTCAAAA 13) The RevCom sequence(5-3) is-103 nt.: CTTTATAGCTAGGGGTGCCTTTGGCTGAGAGATAACATTTCGTTATTAACCCTTAAAACCTGATCTGGATAATACCAGCGTAGGAAAGCCTGTAGAAAGTTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: AAAACTTTCTACAGGCTTTCCTACGCTGGTATTATCCAGATCAGGTTTTAAGGGTTAATAAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: CTTTATAGCTAGGGGTGCCTTTGGCTGAGAGATAACATTTCGTTATTAACCCTTAAAACCTG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -17.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.53 kcal/mol. The frequency of the MFE structure in the ensemble is 6.08 %. The ensemble diversity is 21.53. The centroid secondary structure in dot-bracket notation with a minimum free energy of -11.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium perfringens , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

CT09821

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RiboSwitch type

TPP type switch

Bacteria strain target

Clostridium tetani

Length of Switch in nucleotides

109

Sequence

AAATAAATTTAGGGGAGCTTATAAAAATAGGCTGAGAAAGAGATGTTATCTCTGACCCTCATAACCTGATTTGGCTAATACCAACGTAGGGAACATTGTGTATTGTAGT

Above is displayed the nucleotide sequence of the Clostridium tetani , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 38 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 109 nt. 8) CG percentage of the sequence= 35.78% 9) *Melting temperature of the DNA based on the Wallace formula= 73.40oC 10) The entered DNA sequence(5-3) is-109 nt.: AAATAAATTTAGGGGAGCTTATAAAAATAGGCTGAGAAAGAGATGTTATCTCTGACCCTCATAACCTGATTTGGCTAATACCAACGTAGGGAACATTGTGTATTGTAGT 11) The complementary(Com) sequence(3-5) is-109 nt.: TTTATTTAAATCCCCTCGAATATTTTTATCCGACTCTTTCTCTACAATAGAGACTGGGAGTATTGGACTAAACCGATTATGGTTGCATCCCTTGTAACACATAACATCA 12) The reverse(Rev) sequence(3-5) is-109 nt.: TGATGTTATGTGTTACAAGGGATGCAACCATAATCGGTTTAGTCCAATACTCCCAGTCTCTATTGTAGAGAAAGAGTCGGATAAAAATATTCGAGGGGATTTAAATAAA 13) The RevCom sequence(5-3) is-109 nt.: ACTACAATACACAATGTTCCCTACGTTGGTATTAGCCAAATCAGGTTATGAGGGTCAGAGATAACATCTCTTTCTCAGCCTATTTTTATAAGCTCCCCTAAATTTATTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: AAATAAATTTAGGGGAGCTTATAAAAATAGGCTGAGAAAGAGATGTTATCTCTGACCCTCATAAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: ACTACAATACACAATGTTCCCTACGTTGGTATTAGCCAAATCAGGTTATGAGGGTCAGAGATAAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -24.59 kcal/mol. The frequency of the MFE structure in the ensemble is 1.76 %. The ensemble diversity is 24.45. The centroid secondary structure in dot-bracket notation with a minimum free energy of -17.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

CD88821

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RiboSwitch type

TPP type switch

Bacteria strain target

Corynebacterium diphtheriae

Length of Switch in nucleotides

113

Sequence

ACGAGATGCCCGGGTGCCATGTGCTTGCTGTACGTGGCTGAGACGGCTGTTTGGCCGAACCGTAGAACCTGATCTGGGTAATACCAGCGATAGGAAGACTTCATACTGTGACT

Above is displayed the nucleotide sequence of the Corynebacterium diphtheriae , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 25 nt. 2) Cytosine(C) in the sequence= 26 nt. 3) Guanine(G) in the sequence= 35 nt. 4) Thiamine(T) in the sequence= 27 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 113 nt. 8) CG percentage of the sequence= 53.98% 9) *Melting temperature of the DNA based on the Wallace formula= 81.08oC 10) The entered DNA sequence(5-3) is-113 nt.: ACGAGATGCCCGGGTGCCATGTGCTTGCTGTACGTGGCTGAGACGGCTGTTTGGCCGAACCGTAGAACCTGATCTGGGTAATACCAGCGATAGGAAGACTTCATACTGTGACT 11) The complementary(Com) sequence(3-5) is-113 nt.: TGCTCTACGGGCCCACGGTACACGAACGACATGCACCGACTCTGCCGACAAACCGGCTTGGCATCTTGGACTAGACCCATTATGGTCGCTATCCTTCTGAAGTATGACACTGA 12) The reverse(Rev) sequence(3-5) is-113 nt.: TCAGTGTCATACTTCAGAAGGATAGCGACCATAATGGGTCTAGTCCAAGATGCCAAGCCGGTTTGTCGGCAGAGTCGGTGCATGTCGTTCGTGTACCGTGGGCCCGTAGAGCA 13) The RevCom sequence(5-3) is-113 nt.: AGTCACAGTATGAAGTCTTCCTATCGCTGGTATTACCCAGATCAGGTTCTACGGTTCGGCCAAACAGCCGTCTCAGCCACGTACAGCAAGCACATGGCACCCGGGCATCTCGT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-67 nt.: ACGAGATGCCCGGGTGCCATGTGCTTGCTGTACGTGGCTGAGACGGCTGTTTGGCCGAACCGTAGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-67 nt.: AGTCACAGTATGAAGTCTTCCTATCGCTGGTATTACCCAGATCAGGTTCTACGGTTCGGCCAAACAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Corynebacterium diphtheriae , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Corynebacterium diphtheriae , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -34.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -36.21 kcal/mol. The frequency of the MFE structure in the ensemble is 8.60 %. The ensemble diversity is 15.11. The centroid secondary structure in dot-bracket notation with a minimum free energy of -32.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Corynebacterium diphtheriae , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Corynebacterium diphtheriae , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

EF818299

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RiboSwitch type

TPP type switch

Bacteria strain target

Enterococcus faecalis

Length of Switch in nucleotides

Sequence

CAAAGTAAATCGGCATTTCCCTGCGACAGTACTAACTGCATCAGGTTCAATGGGTATCATCTCAGCCATAACAGCACCCCAAATGTTTTTT

Above is displayed the nucleotide sequence of the Enterococcus faecalis , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 15 nt. 4) Thiamine(T) in the sequence= 25 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 91 nt. 8) CG percentage of the sequence= 42.86% 9) *Melting temperature of the DNA based on the Wallace formula= 75.08oC 10) The entered DNA sequence(5-3) is-91 nt.: CAAAGTAAATCGGCATTTCCCTGCGACAGTACTAACTGCATCAGGTTCAATGGGTATCATCTCAGCCATAACAGCACCCCAAATGTTTTTT 11) The complementary(Com) sequence(3-5) is-91 nt.: GTTTCATTTAGCCGTAAAGGGACGCTGTCATGATTGACGTAGTCCAAGTTACCCATAGTAGAGTCGGTATTGTCGTGGGGTTTACAAAAAA 12) The reverse(Rev) sequence(3-5) is-91 nt.: TTTTTTGTAAACCCCACGACAATACCGACTCTACTATGGGTAACTTGGACTACGTCAATCATGACAGCGTCCCTTTACGGCTAAATGAAAC 13) The RevCom sequence(5-3) is-91 nt.: AAAAAACATTTGGGGTGCTGTTATGGCTGAGATGATACCCATTGAACCTGATGCAGTTAGTACTGTCGCAGGGAAATGCCGATTTACTTTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-56 nt.: CAAAGTAAATCGGCATTTCCCTGCGACAGTACTAACTGCATCAGGTTCAATGGGTA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-56 nt.: AAAAAACATTTGGGGTGCTGTTATGGCTGAGATGATACCCATTGAACCTGATGCAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecalis , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecalis , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -13.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -14.56 kcal/mol. The frequency of the MFE structure in the ensemble is 9.29 %. The ensemble diversity is 14.13. The centroid secondary structure in dot-bracket notation with a minimum free energy of -13.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecalis , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecalis , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

EF78419

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RiboSwitch type

TPP type switch

Bacteria strain target

Enterococcus faecium

Length of Switch in nucleotides

103

Sequence

CAGCTGTTTATTCACAATTCCTACGCTCGCATAACCGATACAGGTACGAAGGGTTTAGAAATAGATTCAATCTCAGCCCAATTGGACTCCCCTTTGTGAGTTT

Above is displayed the nucleotide sequence of the Enterococcus faecium , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 28 nt. 2) Cytosine(C) in the sequence= 25 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 103 nt. 8) CG percentage of the sequence= 42.72% 9) *Melting temperature of the DNA based on the Wallace formula= 75.89oC 10) The entered DNA sequence(5-3) is-103 nt.: CAGCTGTTTATTCACAATTCCTACGCTCGCATAACCGATACAGGTACGAAGGGTTTAGAAATAGATTCAATCTCAGCCCAATTGGACTCCCCTTTGTGAGTTT 11) The complementary(Com) sequence(3-5) is-103 nt.: GTCGACAAATAAGTGTTAAGGATGCGAGCGTATTGGCTATGTCCATGCTTCCCAAATCTTTATCTAAGTTAGAGTCGGGTTAACCTGAGGGGAAACACTCAAA 12) The reverse(Rev) sequence(3-5) is-103 nt.: TTTGAGTGTTTCCCCTCAGGTTAACCCGACTCTAACTTAGATAAAGATTTGGGAAGCATGGACATAGCCAATACGCTCGCATCCTTAACACTTATTTGTCGAC 13) The RevCom sequence(5-3) is-103 nt.: AAACTCACAAAGGGGAGTCCAATTGGGCTGAGATTGAATCTATTTCTAAACCCTTCGTACCTGTATCGGTTATGCGAGCGTAGGAATTGTGAATAAACAGCTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: CAGCTGTTTATTCACAATTCCTACGCTCGCATAACCGATACAGGTACGAAGGGTTTAGAAAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: AAACTCACAAAGGGGAGTCCAATTGGGCTGAGATTGAATCTATTTCTAAACCCTTCGTACCT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecium , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecium , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -18.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.99 kcal/mol. The frequency of the MFE structure in the ensemble is 7.56 %. The ensemble diversity is 19.24. The centroid secondary structure in dot-bracket notation with a minimum free energy of -17.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecium , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecium , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

ET74429

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RiboSwitch type

TPP type switch

Bacteria strain target

Francisella tularensis

Length of Switch in nucleotides

102

Sequence

AAAGATAACCAAACAAACTCCCTACGCTAATATTACTTAGATCAGGTACAAAGGGTCACTTCTCAGCCATTTTTAATAAAAACAGCACCCCTGTTGTCTTTT

Above is displayed the nucleotide sequence of the Francisella tularensis , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 25 nt. 3) Guanine(G) in the sequence= 12 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 102 nt. 8) CG percentage of the sequence= 36.27% 9) *Melting temperature of the DNA based on the Wallace formula= 73.18oC 10) The entered DNA sequence(5-3) is-102 nt.: AAAGATAACCAAACAAACTCCCTACGCTAATATTACTTAGATCAGGTACAAAGGGTCACTTCTCAGCCATTTTTAATAAAAACAGCACCCCTGTTGTCTTTT 11) The complementary(Com) sequence(3-5) is-102 nt.: TTTCTATTGGTTTGTTTGAGGGATGCGATTATAATGAATCTAGTCCATGTTTCCCAGTGAAGAGTCGGTAAAAATTATTTTTGTCGTGGGGACAACAGAAAA 12) The reverse(Rev) sequence(3-5) is-102 nt.: TTTTCTGTTGTCCCCACGACAAAAATAATTTTTACCGACTCTTCACTGGGAAACATGGACTAGATTCATTATAATCGCATCCCTCAAACAAACCAATAGAAA 13) The RevCom sequence(5-3) is-102 nt.: AAAAGACAACAGGGGTGCTGTTTTTATTAAAAATGGCTGAGAAGTGACCCTTTGTACCTGATCTAAGTAATATTAGCGTAGGGAGTTTGTTTGGTTATCTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: AAAGATAACCAAACAAACTCCCTACGCTAATATTACTTAGATCAGGTACAAAGGGTCACTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: AAAAGACAACAGGGGTGCTGTTTTTATTAAAAATGGCTGAGAAGTGACCCTTTGTACCTGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Francisella tularensis , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Francisella tularensis , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -13.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -14.73 kcal/mol. The frequency of the MFE structure in the ensemble is 8.34 %. The ensemble diversity is 11.68. The centroid secondary structure in dot-bracket notation with a minimum free energy of -12.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Francisella tularensis , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Francisella tularensis , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

HI12529

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RiboSwitch type

TPP type switch

Bacteria strain target

Haemophilus influenzae

Length of Switch in nucleotides

Sequence

AAAGCCTAGTCGGGGTGCAATACGCTGAGATCATACCCGTGAACCTGAAACAGTTAATACTGACGTAGGAAACTAGGAATATAACCTT

Above is displayed the nucleotide sequence of the Haemophilus influenzae , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 18 nt. 3) Guanine(G) in the sequence= 20 nt. 4) Thiamine(T) in the sequence= 19 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 88 nt. 8) CG percentage of the sequence= 43.18% 9) *Melting temperature of the DNA based on the Wallace formula= 74.96oC 10) The entered DNA sequence(5-3) is-88 nt.: AAAGCCTAGTCGGGGTGCAATACGCTGAGATCATACCCGTGAACCTGAAACAGTTAATACTGACGTAGGAAACTAGGAATATAACCTT 11) The complementary(Com) sequence(3-5) is-88 nt.: TTTCGGATCAGCCCCACGTTATGCGACTCTAGTATGGGCACTTGGACTTTGTCAATTATGACTGCATCCTTTGATCCTTATATTGGAA 12) The reverse(Rev) sequence(3-5) is-88 nt.: TTCCAATATAAGGATCAAAGGATGCAGTCATAATTGACAAAGTCCAAGTGCCCATACTAGAGTCGCATAACGTGGGGCTGATCCGAAA 13) The RevCom sequence(5-3) is-88 nt.: AAGGTTATATTCCTAGTTTCCTACGTCAGTATTAACTGTTTCAGGTTCACGGGTATGATCTCAGCGTATTGCACCCCGACTAGGCTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-54 nt.: AAAGCCTAGTCGGGGTGCAATACGCTGAGATCATACCCGTGAACCTGAAACAGT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-54 nt.: AAGGTTATATTCCTAGTTTCCTACGTCAGTATTAACTGTTTCAGGTTCACGGGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Haemophilus influenzae , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Haemophilus influenzae , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -19.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -20.60 kcal/mol. The frequency of the MFE structure in the ensemble is 16.68 %. The ensemble diversity is 8.38. The centroid secondary structure in dot-bracket notation with a minimum free energy of -19.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Haemophilus influenzae , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Haemophilus influenzae , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

HP12119

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RiboSwitch type

TPP type switch

Bacteria strain target

Helicobacter pylori

Length of Switch in nucleotides

110

Sequence

GGAGCATTTAAGGGGTGCTTTTTAAAACGCTCAAGTTTTTAAAAGGCTGAGATCAAACCCGTAGAACTTGTCAAGGTAATTCTTGCGTAAGGAAATAGCATGTTAATAAC

Above is displayed the nucleotide sequence of the Helicobacter pylori , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 37 nt. 2) Cytosine(C) in the sequence= 16 nt. 3) Guanine(G) in the sequence= 25 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 110 nt. 8) CG percentage of the sequence= 37.27% 9) *Melting temperature of the DNA based on the Wallace formula= 74.07oC 10) The entered DNA sequence(5-3) is-110 nt.: GGAGCATTTAAGGGGTGCTTTTTAAAACGCTCAAGTTTTTAAAAGGCTGAGATCAAACCCGTAGAACTTGTCAAGGTAATTCTTGCGTAAGGAAATAGCATGTTAATAAC 11) The complementary(Com) sequence(3-5) is-110 nt.: CCTCGTAAATTCCCCACGAAAAATTTTGCGAGTTCAAAAATTTTCCGACTCTAGTTTGGGCATCTTGAACAGTTCCATTAAGAACGCATTCCTTTATCGTACAATTATTG 12) The reverse(Rev) sequence(3-5) is-110 nt.: CAATAATTGTACGATAAAGGAATGCGTTCTTAATGGAACTGTTCAAGATGCCCAAACTAGAGTCGGAAAATTTTTGAACTCGCAAAATTTTTCGTGGGGAATTTACGAGG 13) The RevCom sequence(5-3) is-110 nt.: GTTATTAACATGCTATTTCCTTACGCAAGAATTACCTTGACAAGTTCTACGGGTTTGATCTCAGCCTTTTAAAAACTTGAGCGTTTTAAAAAGCACCCCTTAAATGCTCC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: GGAGCATTTAAGGGGTGCTTTTTAAAACGCTCAAGTTTTTAAAAGGCTGAGATCAAACCCGTAGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: GTTATTAACATGCTATTTCCTTACGCAAGAATTACCTTGACAAGTTCTACGGGTTTGATCTCAGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Helicobacter pylori , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Helicobacter pylori , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -18.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -21.76 kcal/mol. The frequency of the MFE structure in the ensemble is 0.31 %. The ensemble diversity is 25.51. The centroid secondary structure in dot-bracket notation with a minimum free energy of -15.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Helicobacter pylori , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Helicobacter pylori , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

KP63390

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RiboSwitch type

TPP type switch

Bacteria strain target

Klebsiella pneumoniae

Length of Switch in nucleotides

220

Sequence

TTTTGAGTGAGCCTCAAATCCCTTCGCCGGCGTTATCCGGATCAGGTTCGACGGGTATTTTCTCAGCCCATGCGCTTCATCCTTCAAGCCGCATCTGCGTTAGCTTCGCGCGTTCACCCCAGTCACATAGTTATCTATGCTCCAGGGGATTCATCCGCTTGCTGCCTTGATGCAACTTGAATGATATTGCGTATGTTTATTAGCACCCCGTTGAGAACGG

Above is displayed the nucleotide sequence of the Klebsiella pneumoniae , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 41 nt. 2) Cytosine(C) in the sequence= 62 nt. 3) Guanine(G) in the sequence= 50 nt. 4) Thiamine(T) in the sequence= 67 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 220 nt. 8) CG percentage of the sequence= 50.91% 9) *Melting temperature of the DNA based on the Wallace formula= 82.72oC 10) The entered DNA sequence(5-3) is-220 nt.: TTTTGAGTGAGCCTCAAATCCCTTCGCCGGCGTTATCCGGATCAGGTTCGACGGGTATTTTCTCAGCCCATGCGCTTCATCCTTCAAGCCGCATCTGCGTTAGCTTCGCGCGTTCACCCCAGTCACATAGTTATCTATGCTCCAGGGGATTCATCCGCTTGCTGCCTTGATGCAACTTGAATGATATTGCGTATGTTTATTAGCACCCCGTTGAGAACGG 11) The complementary(Com) sequence(3-5) is-220 nt.: AAAACTCACTCGGAGTTTAGGGAAGCGGCCGCAATAGGCCTAGTCCAAGCTGCCCATAAAAGAGTCGGGTACGCGAAGTAGGAAGTTCGGCGTAGACGCAATCGAAGCGCGCAAGTGGGGTCAGTGTATCAATAGATACGAGGTCCCCTAAGTAGGCGAACGACGGAACTACGTTGAACTTACTATAACGCATACAAATAATCGTGGGGCAACTCTTGCC 12) The reverse(Rev) sequence(3-5) is-220 nt.: GGCAAGAGTTGCCCCACGATTATTTGTATGCGTTATAGTAAGTTCAACGTAGTTCCGTCGTTCGCCTACTTAGGGGACCTCGTATCTATTGATACACTGACCCCACTTGCGCGCTTCGATTGCGTCTACGCCGAACTTCCTACTTCGCGTACCCGACTCTTTTATGGGCAGCTTGGACTAGGCCTATTGCGGCCGCTTCCCTAAACTCCGAGTGAGTTTT 13) The RevCom sequence(5-3) is-220 nt.: CCGTTCTCAACGGGGTGCTAATAAACATACGCAATATCATTCAAGTTGCATCAAGGCAGCAAGCGGATGAATCCCCTGGAGCATAGATAACTATGTGACTGGGGTGAACGCGCGAAGCTAACGCAGATGCGGCTTGAAGGATGAAGCGCATGGGCTGAGAAAATACCCGTCGAACCTGATCCGGATAACGCCGGCGAAGGGATTTGAGGCTCACTCAAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-120 nt.: TTTTGAGTGAGCCTCAAATCCCTTCGCCGGCGTTATCCGGATCAGGTTCGACGGGTATTTTCTCAGCCCATGCGCTTCATCCTTCAAGCCGCATCTGCGTTAGCTTCGCGCGTTCACCCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-120 nt.: CCGTTCTCAACGGGGTGCTAATAAACATACGCAATATCATTCAAGTTGCATCAAGGCAGCAAGCGGATGAATCCCCTGGAGCATAGATAACTATGTGACTGGGGTGAACGCGCGAAGCTA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Klebsiella pneumoniae , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Klebsiella pneumoniae , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -67.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -70.07 kcal/mol. The frequency of the MFE structure in the ensemble is 2.50 %. The ensemble diversity is 9.26. The centroid secondary structure in dot-bracket notation with a minimum free energy of -65.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Klebsiella pneumoniae , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Klebsiella pneumoniae , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

LP14318

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RiboSwitch type

TPP type switch

Bacteria strain target

Legionella pneumophila

Length of Switch in nucleotides

Sequence

TTAGATGGCGCGGGGTGTCGGGAAATCCGGCTGAGAGTTACCCGTTGAACTTGATCTGAATCATATCAGCGTAAGGACGCCTTCAAAAAAACCA

Above is displayed the nucleotide sequence of the Legionella pneumophila , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 20 nt. 3) Guanine(G) in the sequence= 26 nt. 4) Thiamine(T) in the sequence= 21 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 94 nt. 8) CG percentage of the sequence= 48.94% 9) *Melting temperature of the DNA based on the Wallace formula= 77.81oC 10) The entered DNA sequence(5-3) is-94 nt.: TTAGATGGCGCGGGGTGTCGGGAAATCCGGCTGAGAGTTACCCGTTGAACTTGATCTGAATCATATCAGCGTAAGGACGCCTTCAAAAAAACCA 11) The complementary(Com) sequence(3-5) is-94 nt.: AATCTACCGCGCCCCACAGCCCTTTAGGCCGACTCTCAATGGGCAACTTGAACTAGACTTAGTATAGTCGCATTCCTGCGGAAGTTTTTTTGGT 12) The reverse(Rev) sequence(3-5) is-94 nt.: ACCAAAAAAACTTCCGCAGGAATGCGACTATACTAAGTCTAGTTCAAGTTGCCCATTGAGAGTCGGCCTAAAGGGCTGTGGGGCGCGGTAGATT 13) The RevCom sequence(5-3) is-94 nt.: TGGTTTTTTTGAAGGCGTCCTTACGCTGATATGATTCAGATCAAGTTCAACGGGTAACTCTCAGCCGGATTTCCCGACACCCCGCGCCATCTAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-57 nt.: TTAGATGGCGCGGGGTGTCGGGAAATCCGGCTGAGAGTTACCCGTTGAACTTGATCT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-57 nt.: TGGTTTTTTTGAAGGCGTCCTTACGCTGATATGATTCAGATCAAGTTCAACGGGTAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Legionella pneumophila , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Legionella pneumophila , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -23.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -24.71 kcal/mol. The frequency of the MFE structure in the ensemble is 6.23 %. The ensemble diversity is 16.41. The centroid secondary structure in dot-bracket notation with a minimum free energy of -21.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Legionella pneumophila , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Legionella pneumophila , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

LI61198

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RiboSwitch type

TPP type switch

Bacteria strain target

Leptospira interrogans

Length of Switch in nucleotides

Sequence

AATTTTACAGGTCCGTTTTCCTACGCAGGTCTTATCCTGATCAGGTTCCGGGGACTCTCTCAGAGATTCACGCAGTGAATCCCACCCCCAACGTCCAAG

Above is displayed the nucleotide sequence of the Leptospira interrogans , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 22 nt. 2) Cytosine(C) in the sequence= 31 nt. 3) Guanine(G) in the sequence= 20 nt. 4) Thiamine(T) in the sequence= 26 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 99 nt. 8) CG percentage of the sequence= 51.52% 9) *Melting temperature of the DNA based on the Wallace formula= 79.23oC 10) The entered DNA sequence(5-3) is-99 nt.: AATTTTACAGGTCCGTTTTCCTACGCAGGTCTTATCCTGATCAGGTTCCGGGGACTCTCTCAGAGATTCACGCAGTGAATCCCACCCCCAACGTCCAAG 11) The complementary(Com) sequence(3-5) is-99 nt.: TTAAAATGTCCAGGCAAAAGGATGCGTCCAGAATAGGACTAGTCCAAGGCCCCTGAGAGAGTCTCTAAGTGCGTCACTTAGGGTGGGGGTTGCAGGTTC 12) The reverse(Rev) sequence(3-5) is-99 nt.: GAACCTGCAACCCCCACCCTAAGTGACGCACTTAGAGACTCTCTCAGGGGCCTTGGACTAGTCCTATTCTGGACGCATCCTTTTGCCTGGACATTTTAA 13) The RevCom sequence(5-3) is-99 nt.: CTTGGACGTTGGGGGTGGGATTCACTGCGTGAATCTCTGAGAGAGTCCCCGGAACCTGATCAGGATAAGACCTGCGTAGGAAAACGGACCTGTAAAATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: AATTTTACAGGTCCGTTTTCCTACGCAGGTCTTATCCTGATCAGGTTCCGGGGACTCTCT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: CTTGGACGTTGGGGGTGGGATTCACTGCGTGAATCTCTGAGAGAGTCCCCGGAACCTGAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Leptospira interrogans , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Leptospira interrogans , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.92 kcal/mol. The frequency of the MFE structure in the ensemble is 16.33 %. The ensemble diversity is 13.89. The centroid secondary structure in dot-bracket notation with a minimum free energy of -14.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Leptospira interrogans , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Leptospira interrogans , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

LM65238

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RiboSwitch type

TPP type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

106

Sequence

AAGAAAAACTAGGGGGGCCGATTCTGGCTGAGATAGGAAGGTAATGCTTTCTGACCCTTTGAACCTGTTTGTTAGTGCAAGCGTAGGGAAGTGAATGTGAAAGTGA

Above is displayed the nucleotide sequence of the Listeria monocytogenes , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 14 nt. 3) Guanine(G) in the sequence= 34 nt. 4) Thiamine(T) in the sequence= 27 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 106 nt. 8) CG percentage of the sequence= 45.28% 9) *Melting temperature of the DNA based on the Wallace formula= 77.12oC 10) The entered DNA sequence(5-3) is-106 nt.: AAGAAAAACTAGGGGGGCCGATTCTGGCTGAGATAGGAAGGTAATGCTTTCTGACCCTTTGAACCTGTTTGTTAGTGCAAGCGTAGGGAAGTGAATGTGAAAGTGA 11) The complementary(Com) sequence(3-5) is-106 nt.: TTCTTTTTGATCCCCCCGGCTAAGACCGACTCTATCCTTCCATTACGAAAGACTGGGAAACTTGGACAAACAATCACGTTCGCATCCCTTCACTTACACTTTCACT 12) The reverse(Rev) sequence(3-5) is-106 nt.: AGTGAAAGTGTAAGTGAAGGGATGCGAACGTGATTGTTTGTCCAAGTTTCCCAGTCTTTCGTAATGGAAGGATAGAGTCGGTCTTAGCCGGGGGGATCAAAAAGAA 13) The RevCom sequence(5-3) is-106 nt.: TCACTTTCACATTCACTTCCCTACGCTTGCACTAACAAACAGGTTCAAAGGGTCAGAAAGCATTACCTTCCTATCTCAGCCAGAATCGGCCCCCCTAGTTTTTCTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-63 nt.: AAGAAAAACTAGGGGGGCCGATTCTGGCTGAGATAGGAAGGTAATGCTTTCTGACCCTTTGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-63 nt.: TCACTTTCACATTCACTTCCCTACGCTTGCACTAACAAACAGGTTCAAAGGGTCAGAAAGCAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -23.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -25.23 kcal/mol. The frequency of the MFE structure in the ensemble is 5.12 %. The ensemble diversity is 16.39. The centroid secondary structure in dot-bracket notation with a minimum free energy of -17.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

ML12138

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RiboSwitch type

TPP type switch

Bacteria strain target

Mycobacterium leprae

Length of Switch in nucleotides

139

Sequence

CTGACGGCATCTTGAACCTCCCTTCGCCGGCATGACCCGGATCAGGTGTGGGAGGGTAAGGGTAGGTTCAGTCACTCTGGCTGTGCCCACTCTCAGCCCCGCAGATTCGGACTGCCTGGGGACTCCCGTGTACTGAAGT

Above is displayed the nucleotide sequence of the Mycobacterium leprae , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 23 nt. 2) Cytosine(C) in the sequence= 42 nt. 3) Guanine(G) in the sequence= 43 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 139 nt. 8) CG percentage of the sequence= 61.15% 9) *Melting temperature of the DNA based on the Wallace formula= 85.13oC 10) The entered DNA sequence(5-3) is-139 nt.: CTGACGGCATCTTGAACCTCCCTTCGCCGGCATGACCCGGATCAGGTGTGGGAGGGTAAGGGTAGGTTCAGTCACTCTGGCTGTGCCCACTCTCAGCCCCGCAGATTCGGACTGCCTGGGGACTCCCGTGTACTGAAGT 11) The complementary(Com) sequence(3-5) is-139 nt.: GACTGCCGTAGAACTTGGAGGGAAGCGGCCGTACTGGGCCTAGTCCACACCCTCCCATTCCCATCCAAGTCAGTGAGACCGACACGGGTGAGAGTCGGGGCGTCTAAGCCTGACGGACCCCTGAGGGCACATGACTTCA 12) The reverse(Rev) sequence(3-5) is-139 nt.: TGAAGTCATGTGCCCTCAGGGGTCCGTCAGGCTTAGACGCCCCGACTCTCACCCGTGTCGGTCTCACTGACTTGGATGGGAATGGGAGGGTGTGGACTAGGCCCAGTACGGCCGCTTCCCTCCAAGTTCTACGGCAGTC 13) The RevCom sequence(5-3) is-139 nt.: ACTTCAGTACACGGGAGTCCCCAGGCAGTCCGAATCTGCGGGGCTGAGAGTGGGCACAGCCAGAGTGACTGAACCTACCCTTACCCTCCCACACCTGATCCGGGTCATGCCGGCGAAGGGAGGTTCAAGATGCCGTCAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-80 nt.: CTGACGGCATCTTGAACCTCCCTTCGCCGGCATGACCCGGATCAGGTGTGGGAGGGTAAGGGTAGGTTCAGTCACTCTGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-80 nt.: ACTTCAGTACACGGGAGTCCCCAGGCAGTCCGAATCTGCGGGGCTGAGAGTGGGCACAGCCAGAGTGACTGAACCTACCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Mycobacterium leprae , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Mycobacterium leprae , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -48.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -51.24 kcal/mol. The frequency of the MFE structure in the ensemble is 1.38 %. The ensemble diversity is 37.75. The centroid secondary structure in dot-bracket notation with a minimum free energy of -37.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Mycobacterium leprae , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Mycobacterium leprae , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

MT67637

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RiboSwitch type

TPP type switch

Bacteria strain target

Mycobacterium tuberculosis

Length of Switch in nucleotides

111

Sequence

TGATGGTCATTTGCAACTCCCTACGCCGGCATTACCCGGTCAGGTTCGTACGGTCGACGGCCCCGAGCCGTCCTCTCAGCGCACTCGGCGTGCGCTCCCGCGTGGGTACCC

Above is displayed the nucleotide sequence of the Mycobacterium tuberculosis , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 14 nt. 2) Cytosine(C) in the sequence= 42 nt. 3) Guanine(G) in the sequence= 32 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 111 nt. 8) CG percentage of the sequence= 66.67% 9) *Melting temperature of the DNA based on the Wallace formula= 86.18oC 10) The entered DNA sequence(5-3) is-111 nt.: TGATGGTCATTTGCAACTCCCTACGCCGGCATTACCCGGTCAGGTTCGTACGGTCGACGGCCCCGAGCCGTCCTCTCAGCGCACTCGGCGTGCGCTCCCGCGTGGGTACCC 11) The complementary(Com) sequence(3-5) is-111 nt.: ACTACCAGTAAACGTTGAGGGATGCGGCCGTAATGGGCCAGTCCAAGCATGCCAGCTGCCGGGGCTCGGCAGGAGAGTCGCGTGAGCCGCACGCGAGGGCGCACCCATGGG 12) The reverse(Rev) sequence(3-5) is-111 nt.: CCCATGGGTGCGCCCTCGCGTGCGGCTCACGCGACTCTCCTGCCGAGCCCCGGCAGCTGGCATGCTTGGACTGGCCCATTACGGCCGCATCCCTCAACGTTTACTGGTAGT 13) The RevCom sequence(5-3) is-111 nt.: GGGTACCCACGCGGGAGCGCACGCCGAGTGCGCTGAGAGGACGGCTCGGGGCCGTCGACCGTACGAACCTGACCGGGTAATGCCGGCGTAGGGAGTTGCAAATGACCATCA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-66 nt.: TGATGGTCATTTGCAACTCCCTACGCCGGCATTACCCGGTCAGGTTCGTACGGTCGACGGCCCCGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-66 nt.: GGGTACCCACGCGGGAGCGCACGCCGAGTGCGCTGAGAGGACGGCTCGGGGCCGTCGACCGTACGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Mycobacterium tuberculosis , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Mycobacterium tuberculosis , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -37.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -39.63 kcal/mol. The frequency of the MFE structure in the ensemble is 5.11 %. The ensemble diversity is 25.04. The centroid secondary structure in dot-bracket notation with a minimum free energy of -31.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Mycobacterium tuberculosis , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Mycobacterium tuberculosis , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

NG08601

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RiboSwitch type

TPP type switch

Bacteria strain target

Neisseria gonorrhoeae

Length of Switch in nucleotides

104

Sequence

GGCGGGGAGGTTTTGTTTCCTACGCAGGCATTACCCCGACAGGTTCTACGGATTTTGCTTTCGCAATCTCAGCCGCCCGGCGGGCGGCACTCCGACAAGAAGGC

Above is displayed the nucleotide sequence of the Neisseria gonorrhoeae , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 18 nt. 2) Cytosine(C) in the sequence= 31 nt. 3) Guanine(G) in the sequence= 32 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 104 nt. 8) CG percentage of the sequence= 60.58% 9) *Melting temperature of the DNA based on the Wallace formula= 83.27oC 10) The entered DNA sequence(5-3) is-104 nt.: GGCGGGGAGGTTTTGTTTCCTACGCAGGCATTACCCCGACAGGTTCTACGGATTTTGCTTTCGCAATCTCAGCCGCCCGGCGGGCGGCACTCCGACAAGAAGGC 11) The complementary(Com) sequence(3-5) is-104 nt.: CCGCCCCTCCAAAACAAAGGATGCGTCCGTAATGGGGCTGTCCAAGATGCCTAAAACGAAAGCGTTAGAGTCGGCGGGCCGCCCGCCGTGAGGCTGTTCTTCCG 12) The reverse(Rev) sequence(3-5) is-104 nt.: CGGAAGAACAGCCTCACGGCGGGCGGCCCGCCGACTCTAACGCTTTCGTTTTAGGCATCTTGGACAGCCCCATTACGGACGCATCCTTTGTTTTGGAGGGGCGG 13) The RevCom sequence(5-3) is-104 nt.: GCCTTCTTGTCGGAGTGCCGCCCGCCGGGCGGCTGAGATTGCGAAAGCAAAATCCGTAGAACCTGTCGGGGTAATGCCTGCGTAGGAAACAAAACCTCCCCGCC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: GGCGGGGAGGTTTTGTTTCCTACGCAGGCATTACCCCGACAGGTTCTACGGATTTTGCTTTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: GCCTTCTTGTCGGAGTGCCGCCCGCCGGGCGGCTGAGATTGCGAAAGCAAAATCCGTAGAAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Neisseria gonorrhoeae , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Neisseria gonorrhoeae , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -33.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -35.28 kcal/mol. The frequency of the MFE structure in the ensemble is 4.72 %. The ensemble diversity is 22.95. The centroid secondary structure in dot-bracket notation with a minimum free energy of -28.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Neisseria gonorrhoeae , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Neisseria gonorrhoeae , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

NM63321

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RiboSwitch type

TPP type switch

Bacteria strain target

Neisseria meningitidis

Length of Switch in nucleotides

104

Sequence

AGCTCCTTGTCGGAGTGCCGCCGCCGGGCGGCTGAGATTGCGAAAGCAGAATCCGTAGAACCTGTCGGGGTAATGCCTGCGTAGGAAACAAACCGTCAAATGCC

Above is displayed the nucleotide sequence of the Neisseria meningitidis , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 25 nt. 2) Cytosine(C) in the sequence= 28 nt. 3) Guanine(G) in the sequence= 33 nt. 4) Thiamine(T) in the sequence= 18 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 104 nt. 8) CG percentage of the sequence= 58.65% 9) *Melting temperature of the DNA based on the Wallace formula= 82.48oC 10) The entered DNA sequence(5-3) is-104 nt.: AGCTCCTTGTCGGAGTGCCGCCGCCGGGCGGCTGAGATTGCGAAAGCAGAATCCGTAGAACCTGTCGGGGTAATGCCTGCGTAGGAAACAAACCGTCAAATGCC 11) The complementary(Com) sequence(3-5) is-104 nt.: TCGAGGAACAGCCTCACGGCGGCGGCCCGCCGACTCTAACGCTTTCGTCTTAGGCATCTTGGACAGCCCCATTACGGACGCATCCTTTGTTTGGCAGTTTACGG 12) The reverse(Rev) sequence(3-5) is-104 nt.: CCGTAAACTGCCAAACAAAGGATGCGTCCGTAATGGGGCTGTCCAAGATGCCTAAGACGAAAGCGTTAGAGTCGGCGGGCCGCCGCCGTGAGGCTGTTCCTCGA 13) The RevCom sequence(5-3) is-104 nt.: GGCATTTGACGGTTTGTTTCCTACGCAGGCATTACCCCGACAGGTTCTACGGATTCTGCTTTCGCAATCTCAGCCGCCCGGCGGCGGCACTCCGACAAGGAGCT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: AGCTCCTTGTCGGAGTGCCGCCGCCGGGCGGCTGAGATTGCGAAAGCAGAATCCGTAGAACC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: GGCATTTGACGGTTTGTTTCCTACGCAGGCATTACCCCGACAGGTTCTACGGATTCTGCTTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Neisseria meningitidis , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Neisseria meningitidis , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -32.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -34.75 kcal/mol. The frequency of the MFE structure in the ensemble is 1.86 %. The ensemble diversity is 27.77. The centroid secondary structure in dot-bracket notation with a minimum free energy of -21.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Neisseria meningitidis , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Neisseria meningitidis , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

PA00341

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RiboSwitch type

TPP type switch

Bacteria strain target

Pseudomonas aeruginosa

Length of Switch in nucleotides

137

Sequence

TGGCGCGGACATCTTGTTCCCTACGCGGGTTGCTGCGGTCCGCGCGAGGCGGAACCGGACGCTAGCCCGATCAGGTTCAACGGGATCCGGAACTATCCGATCTCAGCCCCTCGTATAGGGCACCCCGACAAGAACCC

Above is displayed the nucleotide sequence of the Pseudomonas aeruginosa , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 26 nt. 2) Cytosine(C) in the sequence= 47 nt. 3) Guanine(G) in the sequence= 41 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 137 nt. 8) CG percentage of the sequence= 64.23% 9) *Melting temperature of the DNA based on the Wallace formula= 86.33oC 10) The entered DNA sequence(5-3) is-137 nt.: TGGCGCGGACATCTTGTTCCCTACGCGGGTTGCTGCGGTCCGCGCGAGGCGGAACCGGACGCTAGCCCGATCAGGTTCAACGGGATCCGGAACTATCCGATCTCAGCCCCTCGTATAGGGCACCCCGACAAGAACCC 11) The complementary(Com) sequence(3-5) is-137 nt.: ACCGCGCCTGTAGAACAAGGGATGCGCCCAACGACGCCAGGCGCGCTCCGCCTTGGCCTGCGATCGGGCTAGTCCAAGTTGCCCTAGGCCTTGATAGGCTAGAGTCGGGGAGCATATCCCGTGGGGCTGTTCTTGGG 12) The reverse(Rev) sequence(3-5) is-137 nt.: CCCAAGAACAGCCCCACGGGATATGCTCCCCGACTCTAGCCTATCAAGGCCTAGGGCAACTTGGACTAGCCCGATCGCAGGCCAAGGCGGAGCGCGCCTGGCGTCGTTGGGCGCATCCCTTGTTCTACAGGCGCGGT 13) The RevCom sequence(5-3) is-137 nt.: GGGTTCTTGTCGGGGTGCCCTATACGAGGGGCTGAGATCGGATAGTTCCGGATCCCGTTGAACCTGATCGGGCTAGCGTCCGGTTCCGCCTCGCGCGGACCGCAGCAACCCGCGTAGGGAACAAGATGTCCGCGCCA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-79 nt.: TGGCGCGGACATCTTGTTCCCTACGCGGGTTGCTGCGGTCCGCGCGAGGCGGAACCGGACGCTAGCCCGATCAGGTTCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-79 nt.: GGGTTCTTGTCGGGGTGCCCTATACGAGGGGCTGAGATCGGATAGTTCCGGATCCCGTTGAACCTGATCGGGCTAGCGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Pseudomonas aeruginosa , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Pseudomonas aeruginosa , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -52.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -54.31 kcal/mol. The frequency of the MFE structure in the ensemble is 5.31 %. The ensemble diversity is 15.86. The centroid secondary structure in dot-bracket notation with a minimum free energy of -49.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Pseudomonas aeruginosa , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Pseudomonas aeruginosa , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

SE012711

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RiboSwitch type

TPP type switch

Bacteria strain target

Salmonella enterica

Length of Switch in nucleotides

101

Sequence

GCCATCTTGTCGGAGTGCCATTTTTGGCTGAGACCGTTAATTCGGGATCCGCGGAACCTGATCAGGTTAATACCTGCGAAGGGAACAAGAGTAATTCTGCT

Above is displayed the nucleotide sequence of the Salmonella enterica , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 24 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 28 nt. 4) Thiamine(T) in the sequence= 27 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 101 nt. 8) CG percentage of the sequence= 49.50% 9) *Melting temperature of the DNA based on the Wallace formula= 78.54oC 10) The entered DNA sequence(5-3) is-101 nt.: GCCATCTTGTCGGAGTGCCATTTTTGGCTGAGACCGTTAATTCGGGATCCGCGGAACCTGATCAGGTTAATACCTGCGAAGGGAACAAGAGTAATTCTGCT 11) The complementary(Com) sequence(3-5) is-101 nt.: CGGTAGAACAGCCTCACGGTAAAAACCGACTCTGGCAATTAAGCCCTAGGCGCCTTGGACTAGTCCAATTATGGACGCTTCCCTTGTTCTCATTAAGACGA 12) The reverse(Rev) sequence(3-5) is-101 nt.: TCGTCTTAATGAGAACAAGGGAAGCGTCCATAATTGGACTAGTCCAAGGCGCCTAGGGCTTAATTGCCAGAGTCGGTTTTTACCGTGAGGCTGTTCTACCG 13) The RevCom sequence(5-3) is-101 nt.: AGCAGAATTACTCTTGTTCCCTTCGCAGGTATTAACCTGATCAGGTTCCGCGGATCCCGAATTAACGGTCTCAGCCAAAAATGGCACTCCGACAAGATGGC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: GCCATCTTGTCGGAGTGCCATTTTTGGCTGAGACCGTTAATTCGGGATCCGCGGAACCTGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: AGCAGAATTACTCTTGTTCCCTTCGCAGGTATTAACCTGATCAGGTTCCGCGGATCCCGAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella enterica , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella enterica , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -27.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -29.47 kcal/mol. The frequency of the MFE structure in the ensemble is 3.47 %. The ensemble diversity is 18.59. The centroid secondary structure in dot-bracket notation with a minimum free energy of -25.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella enterica , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella enterica , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

ST51091

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RiboSwitch type

TPP type switch

Bacteria strain target

Salmonella Typhimurium

Length of Switch in nucleotides

225

Sequence

AGCAGAATTACTCTTGTTCCCTTCGCAGGTATTAACCTGATCAGGTTCCGCGGATCCCGAATTAACGGTCTCAGCCTTTTCCACTTCATCCTTCGCGCTGCCTCTTCGTTGGCTTCGTCCGCTCACTCCAGTCACTTACTTATGTAAGCTCCTGGAGATTCACCGACTTGCCGCCTTGACGCATCACGAACGCTTTTGTGGAAAATTAGCACTCCGACAAGATAA

Above is displayed the nucleotide sequence of the Salmonella Typhimurium , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 47 nt. 2) Cytosine(C) in the sequence= 69 nt. 3) Guanine(G) in the sequence= 43 nt. 4) Thiamine(T) in the sequence= 66 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 225 nt. 8) CG percentage of the sequence= 49.78% 9) *Melting temperature of the DNA based on the Wallace formula= 82.32oC 10) The entered DNA sequence(5-3) is-225 nt.: AGCAGAATTACTCTTGTTCCCTTCGCAGGTATTAACCTGATCAGGTTCCGCGGATCCCGAATTAACGGTCTCAGCCTTTTCCACTTCATCCTTCGCGCTGCCTCTTCGTTGGCTTCGTCCGCTCACTCCAGTCACTTACTTATGTAAGCTCCTGGAGATTCACCGACTTGCCGCCTTGACGCATCACGAACGCTTTTGTGGAAAATTAGCACTCCGACAAGATAA 11) The complementary(Com) sequence(3-5) is-225 nt.: TCGTCTTAATGAGAACAAGGGAAGCGTCCATAATTGGACTAGTCCAAGGCGCCTAGGGCTTAATTGCCAGAGTCGGAAAAGGTGAAGTAGGAAGCGCGACGGAGAAGCAACCGAAGCAGGCGAGTGAGGTCAGTGAATGAATACATTCGAGGACCTCTAAGTGGCTGAACGGCGGAACTGCGTAGTGCTTGCGAAAACACCTTTTAATCGTGAGGCTGTTCTATT 12) The reverse(Rev) sequence(3-5) is-225 nt.: AATAGAACAGCCTCACGATTAAAAGGTGTTTTCGCAAGCACTACGCAGTTCCGCCGTTCAGCCACTTAGAGGTCCTCGAATGTATTCATTCACTGACCTCACTCGCCTGCTTCGGTTGCTTCTCCGTCGCGCTTCCTACTTCACCTTTTCCGACTCTGGCAATTAAGCCCTAGGCGCCTTGGACTAGTCCAATTATGGACGCTTCCCTTGTTCTCATTAAGACGA 13) The RevCom sequence(5-3) is-225 nt.: TTATCTTGTCGGAGTGCTAATTTTCCACAAAAGCGTTCGTGATGCGTCAAGGCGGCAAGTCGGTGAATCTCCAGGAGCTTACATAAGTAAGTGACTGGAGTGAGCGGACGAAGCCAACGAAGAGGCAGCGCGAAGGATGAAGTGGAAAAGGCTGAGACCGTTAATTCGGGATCCGCGGAACCTGATCAGGTTAATACCTGCGAAGGGAACAAGAGTAATTCTGCT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-123 nt.: AGCAGAATTACTCTTGTTCCCTTCGCAGGTATTAACCTGATCAGGTTCCGCGGATCCCGAATTAACGGTCTCAGCCTTTTCCACTTCATCCTTCGCGCTGCCTCTTCGTTGGCTTCGTCCGCT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-123 nt.: TTATCTTGTCGGAGTGCTAATTTTCCACAAAAGCGTTCGTGATGCGTCAAGGCGGCAAGTCGGTGAATCTCCAGGAGCTTACATAAGTAAGTGACTGGAGTGAGCGGACGAAGCCAACGAAGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella Typhimurium , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella Typhimurium , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -57.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -60.19 kcal/mol. The frequency of the MFE structure in the ensemble is 2.43 %. The ensemble diversity is 17.33. The centroid secondary structure in dot-bracket notation with a minimum free energy of -57.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella Typhimurium , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella Typhimurium , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

SA332129

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RiboSwitch type

TPP type switch

Bacteria strain target

Staphylococcus aureus

Length of Switch in nucleotides

109

Sequence

AAAATCAATACGCCACTTTCCTACGCCAGTATAAGCTGGATCAGGTTCAAGGAATTTTAAAGGTATCACTTTAATCTCAGCCTTTATCAAGGCACTTCCAGTGGTTTAA

Above is displayed the nucleotide sequence of the Staphylococcus aureus , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 18 nt. 4) Thiamine(T) in the sequence= 33 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 109 nt. 8) CG percentage of the sequence= 38.53% 9) *Melting temperature of the DNA based on the Wallace formula= 74.53oC 10) The entered DNA sequence(5-3) is-109 nt.: AAAATCAATACGCCACTTTCCTACGCCAGTATAAGCTGGATCAGGTTCAAGGAATTTTAAAGGTATCACTTTAATCTCAGCCTTTATCAAGGCACTTCCAGTGGTTTAA 11) The complementary(Com) sequence(3-5) is-109 nt.: TTTTAGTTATGCGGTGAAAGGATGCGGTCATATTCGACCTAGTCCAAGTTCCTTAAAATTTCCATAGTGAAATTAGAGTCGGAAATAGTTCCGTGAAGGTCACCAAATT 12) The reverse(Rev) sequence(3-5) is-109 nt.: AATTTGGTGACCTTCACGGAACTATTTCCGACTCTAATTTCACTATGGAAATTTTAAGGAACTTGGACTAGGTCGAATATGACCGCATCCTTTCACCGCATAACTAAAA 13) The RevCom sequence(5-3) is-109 nt.: TTAAACCACTGGAAGTGCCTTGATAAAGGCTGAGATTAAAGTGATACCTTTAAAATTCCTTGAACCTGATCCAGCTTATACTGGCGTAGGAAAGTGGCGTATTGATTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: AAAATCAATACGCCACTTTCCTACGCCAGTATAAGCTGGATCAGGTTCAAGGAATTTTAAAGGTA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: TTAAACCACTGGAAGTGCCTTGATAAAGGCTGAGATTAAAGTGATACCTTTAAAATTCCTTGAAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -25.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -27.38 kcal/mol. The frequency of the MFE structure in the ensemble is 9.04 %. The ensemble diversity is 7.04. The centroid secondary structure in dot-bracket notation with a minimum free energy of -25.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

SE109901

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RiboSwitch type

TPP type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

110

Sequence

TTTAACCACTGGAAGTGCCTTTGTTTAAGGCTGAGAGTAAAGAACTGACTTTATAATTCCTGGAACCTGATCCAGTTCATACTGGCGTAGGGAAGTGGCGACGCTCAATT

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 30 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 27 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 110 nt. 8) CG percentage of the sequence= 43.64% 9) *Melting temperature of the DNA based on the Wallace formula= 76.68oC 10) The entered DNA sequence(5-3) is-110 nt.: TTTAACCACTGGAAGTGCCTTTGTTTAAGGCTGAGAGTAAAGAACTGACTTTATAATTCCTGGAACCTGATCCAGTTCATACTGGCGTAGGGAAGTGGCGACGCTCAATT 11) The complementary(Com) sequence(3-5) is-110 nt.: AAATTGGTGACCTTCACGGAAACAAATTCCGACTCTCATTTCTTGACTGAAATATTAAGGACCTTGGACTAGGTCAAGTATGACCGCATCCCTTCACCGCTGCGAGTTAA 12) The reverse(Rev) sequence(3-5) is-110 nt.: TTAACTCGCAGCGGTGAAGGGATGCGGTCATACTTGACCTAGTCCAAGGTCCTTAATATTTCAGTCAAGAAATGAGAGTCGGAATTTGTTTCCGTGAAGGTCACCAATTT 13) The RevCom sequence(5-3) is-110 nt.: AATTGAGCGTCGCCACTTCCCTACGCCAGTATGAACTGGATCAGGTTCCAGGAATTATAAAGTCAGTTCTTTACTCTCAGCCTTAAACAAAGGCACTTCCAGTGGTTAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: TTTAACCACTGGAAGTGCCTTTGTTTAAGGCTGAGAGTAAAGAACTGACTTTATAATTCCTGGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: AATTGAGCGTCGCCACTTCCCTACGCCAGTATGAACTGGATCAGGTTCCAGGAATTATAAAGTCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -26.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -27.72 kcal/mol. The frequency of the MFE structure in the ensemble is 7.22 %. The ensemble diversity is 13.05. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis , TPP type switch.

2D_Structure (A) (B)

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

StS340031

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RiboSwitch type

TPP type switch

Bacteria strain target

Staphylococcus saprophyticus

Length of Switch in nucleotides

Sequence

AAACGCTACTAGGGGAGCCAGTTGGCTGAGATGATTAAATTCAGACCCTTACAACCTGATTTGGTTAATACCAACGTAGGAAAGTAGTTTAATCTAAAG

Above is displayed the nucleotide sequence of the Staphylococcus saprophyticus , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 22 nt. 4) Thiamine(T) in the sequence= 26 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 99 nt. 8) CG percentage of the sequence= 39.39% 9) *Melting temperature of the DNA based on the Wallace formula= 74.26oC 10) The entered DNA sequence(5-3) is-99 nt.: AAACGCTACTAGGGGAGCCAGTTGGCTGAGATGATTAAATTCAGACCCTTACAACCTGATTTGGTTAATACCAACGTAGGAAAGTAGTTTAATCTAAAG 11) The complementary(Com) sequence(3-5) is-99 nt.: TTTGCGATGATCCCCTCGGTCAACCGACTCTACTAATTTAAGTCTGGGAATGTTGGACTAAACCAATTATGGTTGCATCCTTTCATCAAATTAGATTTC 12) The reverse(Rev) sequence(3-5) is-99 nt.: GAAATCTAATTTGATGAAAGGATGCAACCATAATTGGTTTAGTCCAACATTCCCAGACTTAAATTAGTAGAGTCGGTTGACCGAGGGGATCATCGCAAA 13) The RevCom sequence(5-3) is-99 nt.: CTTTAGATTAAACTACTTTCCTACGTTGGTATTAACCAAATCAGGTTGTAAGGGTCTGAATTTAATCATCTCAGCCAACTGGCTCCCCTAGTAGCGTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: AAACGCTACTAGGGGAGCCAGTTGGCTGAGATGATTAAATTCAGACCCTTACAACCTGAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: CTTTAGATTAAACTACTTTCCTACGTTGGTATTAACCAAATCAGGTTGTAAGGGTCTGAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus saprophyticus , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus saprophyticus , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.93 kcal/mol. The frequency of the MFE structure in the ensemble is 9.82 %. The ensemble diversity is 8.73. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus saprophyticus , TPP type switch.

2D_Structure (A) (B)

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

SMS332031

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RiboSwitch type

TPP type switch

Bacteria strain target

Streptococcus mutans

Length of Switch in nucleotides

101

Sequence

TCATGAAACGAATCACATTCCCACGCTAGTATTAACTAGATCAGGTCCATAGGATTTTGCAAATGCAATCTCAGCTAAGGTTAGCACTCCTTGTGATATTT

Above is displayed the nucleotide sequence of the Streptococcus mutans , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 101 nt. 8) CG percentage of the sequence= 38.61% 9) *Melting temperature of the DNA based on the Wallace formula= 74.07oC 10) The entered DNA sequence(5-3) is-101 nt.: TCATGAAACGAATCACATTCCCACGCTAGTATTAACTAGATCAGGTCCATAGGATTTTGCAAATGCAATCTCAGCTAAGGTTAGCACTCCTTGTGATATTT 11) The complementary(Com) sequence(3-5) is-101 nt.: AGTACTTTGCTTAGTGTAAGGGTGCGATCATAATTGATCTAGTCCAGGTATCCTAAAACGTTTACGTTAGAGTCGATTCCAATCGTGAGGAACACTATAAA 12) The reverse(Rev) sequence(3-5) is-101 nt.: TTTATAGTGTTCCTCACGATTGGAATCGACTCTAACGTAAACGTTTTAGGATACCTGGACTAGATCAATTATGATCGCACCCTTACACTAAGCAAAGTACT 13) The RevCom sequence(5-3) is-101 nt.: AAATATCACAAGGAGTGCTAACCTTAGCTGAGATTGCATTTGCAAAATCCTATGGACCTGATCTAGTTAATACTAGCGTGGGAATGTGATTCGTTTCATGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: TCATGAAACGAATCACATTCCCACGCTAGTATTAACTAGATCAGGTCCATAGGATTTTGCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: AAATATCACAAGGAGTGCTAACCTTAGCTGAGATTGCATTTGCAAAATCCTATGGACCTGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus mutans , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus mutans , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -18.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.85 kcal/mol. The frequency of the MFE structure in the ensemble is 4.95 %. The ensemble diversity is 14.55. The centroid secondary structure in dot-bracket notation with a minimum free energy of -16.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus mutans , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus mutans , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

SP4120891

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RiboSwitch type

TPP type switch

Bacteria strain target

Streptococcus pneumoniae

Length of Switch in nucleotides

103

Sequence

ATTAGACTAAGTATCGTTCCCTCCGCTGGCATTACCCAGATCAGGTGCGGTCGAAGTTTAACACTTCCTCTCAGACTGTACACAGACTCCCATATATTATATG

Above is displayed the nucleotide sequence of the Streptococcus pneumoniae , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 28 nt. 3) Guanine(G) in the sequence= 18 nt. 4) Thiamine(T) in the sequence= 30 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 103 nt. 8) CG percentage of the sequence= 44.66% 9) *Melting temperature of the DNA based on the Wallace formula= 76.68oC 10) The entered DNA sequence(5-3) is-103 nt.: ATTAGACTAAGTATCGTTCCCTCCGCTGGCATTACCCAGATCAGGTGCGGTCGAAGTTTAACACTTCCTCTCAGACTGTACACAGACTCCCATATATTATATG 11) The complementary(Com) sequence(3-5) is-103 nt.: TAATCTGATTCATAGCAAGGGAGGCGACCGTAATGGGTCTAGTCCACGCCAGCTTCAAATTGTGAAGGAGAGTCTGACATGTGTCTGAGGGTATATAATATAC 12) The reverse(Rev) sequence(3-5) is-103 nt.: GTATATTATATACCCTCAGACACATGTCAGACTCTCCTTCACAATTTGAAGCTGGCGTGGACTAGACCCATTACGGTCGCCTCCCTTGCTATGAATCAGATTA 13) The RevCom sequence(5-3) is-103 nt.: CATATAATATATGGGAGTCTGTGTACAGTCTGAGAGGAAGTGTTAAACTTCGACCGCACCTGATCTGGGTAATGCCAGCGGAGGGAACGATACTTAGTCTAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-62 nt.: ATTAGACTAAGTATCGTTCCCTCCGCTGGCATTACCCAGATCAGGTGCGGTCGAAGTTTAAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: CATATAATATATGGGAGTCTGTGTACAGTCTGAGAGGAAGTGTTAAACTTCGACCGCACCTG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus pneumoniae , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus pneumoniae , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -17.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.49 kcal/mol. The frequency of the MFE structure in the ensemble is 3.36 %. The ensemble diversity is 21.62. The centroid secondary structure in dot-bracket notation with a minimum free energy of -9.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus pneumoniae , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus pneumoniae , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

SP210123

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RiboSwitch type

TPP type switch

Bacteria strain target

Streptococcus pyogenes

Length of Switch in nucleotides

Sequence

TTGATTATTGGTCACAATCCCTACGCTTGTACTAACAAGATCAGGTCCTCAGGATTTCGCAATTGCGATCTCAGCCAAAGCACTCCTTTGTGAAATA

Above is displayed the nucleotide sequence of the Streptococcus pyogenes , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 97 nt. 8) CG percentage of the sequence= 42.27% 9) *Melting temperature of the DNA based on the Wallace formula= 75.30oC 10) The entered DNA sequence(5-3) is-97 nt.: TTGATTATTGGTCACAATCCCTACGCTTGTACTAACAAGATCAGGTCCTCAGGATTTCGCAATTGCGATCTCAGCCAAAGCACTCCTTTGTGAAATA 11) The complementary(Com) sequence(3-5) is-97 nt.: AACTAATAACCAGTGTTAGGGATGCGAACATGATTGTTCTAGTCCAGGAGTCCTAAAGCGTTAACGCTAGAGTCGGTTTCGTGAGGAAACACTTTAT 12) The reverse(Rev) sequence(3-5) is-97 nt.: ATAAAGTGTTTCCTCACGAAACCGACTCTAGCGTTAACGCTTTAGGACTCCTGGACTAGAACAATCATGTTCGCATCCCTAACACTGGTTATTAGTT 13) The RevCom sequence(5-3) is-97 nt.: TATTTCACAAAGGAGTGCTTTGGCTGAGATCGCAATTGCGAAATCCTGAGGACCTGATCTTGTTAGTACAAGCGTAGGGATTGTGACCAATAATCAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-59 nt.: TTGATTATTGGTCACAATCCCTACGCTTGTACTAACAAGATCAGGTCCTCAGGATTTCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-59 nt.: TATTTCACAAAGGAGTGCTTTGGCTGAGATCGCAATTGCGAAATCCTGAGGACCTGATC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus pyogenes , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus pyogenes , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -18.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.70 kcal/mol. The frequency of the MFE structure in the ensemble is 7.48 %. The ensemble diversity is 20.48. The centroid secondary structure in dot-bracket notation with a minimum free energy of -11.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus pyogenes , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Streptococcus pyogenes , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

VC1081803

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RiboSwitch type

TPP type switch

Bacteria strain target

Vibrio cholerae

Length of Switch in nucleotides

Sequence

TTCCACTTGTCGGAGTGCCATTGGGCTGAGACCGTTTATTCGGGATCCGTTGAACCTGATCAGGTTAATACCTGCGAAGGGAACAAGAGAAGACTCTCT

Above is displayed the nucleotide sequence of the Vibrio cholerae, TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 24 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 27 nt. 4) Thiamine(T) in the sequence= 26 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 99 nt. 8) CG percentage of the sequence= 49.49% 9) *Melting temperature of the DNA based on the Wallace formula= 78.40oC 10) The entered DNA sequence(5-3) is-99 nt.: TTCCACTTGTCGGAGTGCCATTGGGCTGAGACCGTTTATTCGGGATCCGTTGAACCTGATCAGGTTAATACCTGCGAAGGGAACAAGAGAAGACTCTCT 11) The complementary(Com) sequence(3-5) is-99 nt.: AAGGTGAACAGCCTCACGGTAACCCGACTCTGGCAAATAAGCCCTAGGCAACTTGGACTAGTCCAATTATGGACGCTTCCCTTGTTCTCTTCTGAGAGA 12) The reverse(Rev) sequence(3-5) is-99 nt.: TCTCTCAGAAGAGAACAAGGGAAGCGTCCATAATTGGACTAGTCCAAGTTGCCTAGGGCTTATTTGCCAGAGTCGGGTTACCGTGAGGCTGTTCACCTT 13) The RevCom sequence(5-3) is-99 nt.: AGAGAGTCTTCTCTTGTTCCCTTCGCAGGTATTAACCTGATCAGGTTCAACGGATCCCGAATAAACGGTCTCAGCCCAATGGCACTCCGACAAGTGGAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: TTCCACTTGTCGGAGTGCCATTGGGCTGAGACCGTTTATTCGGGATCCGTTGAACCTGAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: AGAGAGTCTTCTCTTGTTCCCTTCGCAGGTATTAACCTGATCAGGTTCAACGGATCCCGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Vibrio cholerae, TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Vibrio cholerae, TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -27.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -29.06 kcal/mol. The frequency of the MFE structure in the ensemble is 7.99 %. The ensemble diversity is 31.00. The centroid secondary structure in dot-bracket notation with a minimum free energy of -16.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Vibrio cholerae, TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Vibrio cholerae, TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

YP700811

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RiboSwitch type

TPP type switch

Bacteria strain target

Yersinia pestis

Length of Switch in nucleotides

126

Sequence

AGGCTCTTGTCGGAGTGCCTAGCACCTGCTTTTTTAGGAAAGCAAACGCAGGCTGAGACCGTTAATTCGGGATCCGCGGAACCTGATCGGGTTAATACCCGCGAAGGGAACAAGAGTAATTTATCG

Above is displayed the nucleotide sequence of the Yersinia pestis , TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 28 nt. 3) Guanine(G) in the sequence= 36 nt. 4) Thiamine(T) in the sequence= 29 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 126 nt. 8) CG percentage of the sequence= 50.79% 9) *Melting temperature of the DNA based on the Wallace formula= 80.39oC 10) The entered DNA sequence(5-3) is-126 nt.: AGGCTCTTGTCGGAGTGCCTAGCACCTGCTTTTTTAGGAAAGCAAACGCAGGCTGAGACCGTTAATTCGGGATCCGCGGAACCTGATCGGGTTAATACCCGCGAAGGGAACAAGAGTAATTTATCG 11) The complementary(Com) sequence(3-5) is-126 nt.: TCCGAGAACAGCCTCACGGATCGTGGACGAAAAAATCCTTTCGTTTGCGTCCGACTCTGGCAATTAAGCCCTAGGCGCCTTGGACTAGCCCAATTATGGGCGCTTCCCTTGTTCTCATTAAATAGC 12) The reverse(Rev) sequence(3-5) is-126 nt.: GCTATTTAATGAGAACAAGGGAAGCGCCCATAATTGGGCTAGTCCAAGGCGCCTAGGGCTTAATTGCCAGAGTCGGACGCAAACGAAAGGATTTTTTCGTCCACGATCCGTGAGGCTGTTCTCGGA 13) The RevCom sequence(5-3) is-126 nt.: CGATAAATTACTCTTGTTCCCTTCGCGGGTATTAACCCGATCAGGTTCCGCGGATCCCGAATTAACGGTCTCAGCCTGCGTTTGCTTTCCTAAAAAAGCAGGTGCTAGGCACTCCGACAAGAGCCT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-73 nt.: AGGCTCTTGTCGGAGTGCCTAGCACCTGCTTTTTTAGGAAAGCAAACGCAGGCTGAGACCGTTAATTCGGGAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-73 nt.: CGATAAATTACTCTTGTTCCCTTCGCGGGTATTAACCCGATCAGGTTCCGCGGATCCCGAATTAACGGTCTCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Yersinia pestis , TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Yersinia pestis , TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -41.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -43.50 kcal/mol. The frequency of the MFE structure in the ensemble is 5.39 %. The ensemble diversity is 18.12. The centroid secondary structure in dot-bracket notation with a minimum free energy of -41.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Yersinia pestis , TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Yersinia pestis , TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

EC560081

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RiboSwitch type

TPP type switch

Bacteria strain target

Escherichia coli

Length of Switch in nucleotides

101

Sequence

AGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATT

Above is displayed the nucleotide sequence of the Escherichia coli, TPP type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 22 nt. 4) Thiamine(T) in the sequence= 25 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 101 nt. 8) CG percentage of the sequence= 48.51% 9) *Melting temperature of the DNA based on the Wallace formula= 78.13oC 10) The entered DNA sequence(5-3) is-101 nt.: AGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATT 11) The complementary(Com) sequence(3-5) is-101 nt.: TCGTCTAATTGAGAACAAGGGAAGCGTCCATAATCGGACTAGTCCAAGGCGCCTAGGGCTTATTTGCCAGAGTCGGTCAATTCCGTGAGGCTGTTCTTTAA 12) The reverse(Rev) sequence(3-5) is-101 nt.: TTAAAGAACAGCCTCACGGAATTGACCGACTCTGGCAAATAAGCCCTAGGCGCCTTGGACTAGTCCGATTATGGACGCTTCCCTTGTTCTCAATTAGACGA 13) The RevCom sequence(5-3) is-101 nt.: AATTTCTTGTCGGAGTGCCTTAACTGGCTGAGACCGTTTATTCGGGATCCGCGGAACCTGATCAGGCTAATACCTGCGAAGGGAACAAGAGTTAATCTGCT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-61 nt.: AGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: AATTTCTTGTCGGAGTGCCTTAACTGGCTGAGACCGTTTATTCGGGATCCGCGGAACCTGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Escherichia coli, TPP type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Escherichia coli, TPP type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -23.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -24.50 kcal/mol. The frequency of the MFE structure in the ensemble is 10.32 %. The ensemble diversity is 14.21. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Escherichia coli, TPP type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Escherichia coli, TPP type switch.

Multiple alignment of the TPP type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the TPP type switches involved in.

Multi_resistance strains for the TPP type switches

RiboSwitch_ID:

BA94081

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RiboSwitch type

Cyclic di-GMP I type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

Sequence

CAGCGAGAAAGGCAAACTGATGGAAACATTAGGACGCAAAACTACAGGAGCTAAGGCCGAAAGGCTACGCTAGCCAGTTACCGGA

Above is displayed the nucleotide sequence of the Bacillus anthracis , Cyclic di-GMP I type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 19 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 10 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 85 nt. 8) CG percentage of the sequence= 50.59% 9) *Melting temperature of the DNA based on the Wallace formula= 77.73oC 10) The entered DNA sequence(5-3) is-85 nt.: CAGCGAGAAAGGCAAACTGATGGAAACATTAGGACGCAAAACTACAGGAGCTAAGGCCGAAAGGCTACGCTAGCCAGTTACCGGA 11) The complementary(Com) sequence(3-5) is-85 nt.: GTCGCTCTTTCCGTTTGACTACCTTTGTAATCCTGCGTTTTGATGTCCTCGATTCCGGCTTTCCGATGCGATCGGTCAATGGCCT 12) The reverse(Rev) sequence(3-5) is-85 nt.: AGGCCATTGACCGATCGCATCGGAAAGCCGGAATCGAGGACATCAAAACGCAGGATTACAAAGGTAGTCAAACGGAAAGAGCGAC 13) The RevCom sequence(5-3) is-85 nt.: TCCGGTAACTGGCTAGCGTAGCCTTTCGGCCTTAGCTCCTGTAGTTTTGCGTCCTAATGTTTCCATCAGTTTGCCTTTCTCGCTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-53 nt.: CAGCGAGAAAGGCAAACTGATGGAAACATTAGGACGCAAAACTACAGGAGCTA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-53 nt.: TCCGGTAACTGGCTAGCGTAGCCTTTCGGCCTTAGCTCCTGTAGTTTTGCGTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis , Cyclic di-GMP I type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis , Cyclic di-GMP I type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -18.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.64 kcal/mol. The frequency of the MFE structure in the ensemble is 8.18 %. The ensemble diversity is 10.64. The centroid secondary structure in dot-bracket notation with a minimum free energy of -16.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis , Cyclic di-GMP I type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis , Cyclic di-GMP I type switch.

Multiple alignment of the Cyclic di-GMP I type switches

Below is presented the sequences alignment of all the Cyclic di-GMP I type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Cyclic di-GMP I type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Cyclic di-GMP-I riboswitches and shorter motifs based on the general one: 1) N{0,6}YN{0,4}GGGGN?GCYN{0,9}RGCTGAGAN{0,13}RACCCN?YN?RRACCTGATCYRGN?TN?ATRCYRGCGN?AGGGAN{0,3}RN{0,13} 2) RRACCTGATCYRG Motifs identified amongst the Cyclic di-GMP-I riboswitches based on the sequences alignment: 1) CSYWWARCYVSG 2) CGCAAAGC Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Cyclic di-GMP I type switches involved in.

Multi_resistance strains for the Cyclic di-GMP I type switches

The table displays known human pathogenic bacteria bearing the Cyclic di-GMP I type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

CD165081

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RiboSwitch type

Cyclic di-GMP I type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

Sequence

AAACTAAATAGGCAAATCTAGAGAAATCTAGTGACGCAAAGCTATAGGGACTAAGGTTTATATACATAAACTATGTCAGCCAGTTGCCAAA

Above is displayed the nucleotide sequence of the Clostridium difficile , Cyclic di-GMP I type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 38 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 21 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 91 nt. 8) CG percentage of the sequence= 35.16% 9) *Melting temperature of the DNA based on the Wallace formula= 71.93oC 10) The entered DNA sequence(5-3) is-91 nt.: AAACTAAATAGGCAAATCTAGAGAAATCTAGTGACGCAAAGCTATAGGGACTAAGGTTTATATACATAAACTATGTCAGCCAGTTGCCAAA 11) The complementary(Com) sequence(3-5) is-91 nt.: TTTGATTTATCCGTTTAGATCTCTTTAGATCACTGCGTTTCGATATCCCTGATTCCAAATATATGTATTTGATACAGTCGGTCAACGGTTT 12) The reverse(Rev) sequence(3-5) is-91 nt.: AAACCGTTGACCGACTGTATCAAATACATATATTTGGAATCAGGGATATCGAAACGCAGTGATCTAAAGAGATCTAAACGGATAAATCAAA 13) The RevCom sequence(5-3) is-91 nt.: TTTGGCAACTGGCTGACATAGTTTATGTATATAAACCTTAGTCCCTATAGCTTTGCGTCACTAGATTTCTCTAGATTTGCCTATTTAGTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-56 nt.: AAACTAAATAGGCAAATCTAGAGAAATCTAGTGACGCAAAGCTATAGGGACTAAGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-56 nt.: TTTGGCAACTGGCTGACATAGTTTATGTATATAAACCTTAGTCCCTATAGCTTTGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile , Cyclic di-GMP I type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile , Cyclic di-GMP I type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -16.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -17.92 kcal/mol. The frequency of the MFE structure in the ensemble is 6.16 %. The ensemble diversity is 12.73. The centroid secondary structure in dot-bracket notation with a minimum free energy of -15.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile , Cyclic di-GMP I type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile , Cyclic di-GMP I type switch.

Multiple alignment of the Cyclic di-GMP I type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP I type switches involved in.

Multi_resistance strains for the Cyclic di-GMP I type switches

RiboSwitch_ID:

CB187781

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RiboSwitch type

Cyclic di-GMP I type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

Sequence

ATCGGCAACTGGCTGGCATGGAATTTCTTCTTTAGCCCCTTTAGCTTTGCGTCACTAGATTTCCCTAGCTATGCCTATTAAATTT

Above is displayed the nucleotide sequence of the Clostridium botulinum, Cyclic di-GMP I type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 17 nt. 2) Cytosine(C) in the sequence= 21 nt. 3) Guanine(G) in the sequence= 15 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 85 nt. 8) CG percentage of the sequence= 42.35% 9) *Melting temperature of the DNA based on the Wallace formula= 74.35oC 10) The entered DNA sequence(5-3) is-85 nt.: ATCGGCAACTGGCTGGCATGGAATTTCTTCTTTAGCCCCTTTAGCTTTGCGTCACTAGATTTCCCTAGCTATGCCTATTAAATTT 11) The complementary(Com) sequence(3-5) is-85 nt.: TAGCCGTTGACCGACCGTACCTTAAAGAAGAAATCGGGGAAATCGAAACGCAGTGATCTAAAGGGATCGATACGGATAATTTAAA 12) The reverse(Rev) sequence(3-5) is-85 nt.: TTTAAATTATCCGTATCGATCCCTTTAGATCACTGCGTTTCGATTTCCCCGATTTCTTCTTTAAGGTACGGTCGGTCAACGGCTA 13) The RevCom sequence(5-3) is-85 nt.: AAATTTAATAGGCATAGCTAGGGAAATCTAGTGACGCAAAGCTAAAGGGGCTAAAGAAGAAATTCCATGCCAGCCAGTTGCCGAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-53 nt.: ATCGGCAACTGGCTGGCATGGAATTTCTTCTTTAGCCCCTTTAGCTTTGCGTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-53 nt.: AAATTTAATAGGCATAGCTAGGGAAATCTAGTGACGCAAAGCTAAAGGGGCTA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum, Cyclic di-GMP I type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum, Cyclic di-GMP I type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -18.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -19.29 kcal/mol. The frequency of the MFE structure in the ensemble is 38.20 %. The ensemble diversity is 8.33. The centroid secondary structure in dot-bracket notation with a minimum free energy of -18.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum, Cyclic di-GMP I type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum, Cyclic di-GMP I type switch.

Multiple alignment of the Cyclic di-GMP I type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP I type switches involved in.

Multi_resistance strains for the Cyclic di-GMP I type switches

RiboSwitch_ID:

CP221781

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RiboSwitch type

Cyclic di-GMP I type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

Sequence

TTTGGCAACTGGCTGACATAGTTATAAACCTTAGTCCCTATAGCTTTGCGTCATTAGATTTCTCTAATTTTGCCCATTTTTTTA

Above is displayed the nucleotide sequence of the Clostridium perfringens, Cyclic di-GMP I type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 19 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 12 nt. 4) Thiamine(T) in the sequence= 36 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 84 nt. 8) CG percentage of the sequence= 34.52% 9) *Melting temperature of the DNA based on the Wallace formula= 71.05oC 10) The entered DNA sequence(5-3) is-84 nt.: TTTGGCAACTGGCTGACATAGTTATAAACCTTAGTCCCTATAGCTTTGCGTCATTAGATTTCTCTAATTTTGCCCATTTTTTTA 11) The complementary(Com) sequence(3-5) is-84 nt.: AAACCGTTGACCGACTGTATCAATATTTGGAATCAGGGATATCGAAACGCAGTAATCTAAAGAGATTAAAACGGGTAAAAAAAT 12) The reverse(Rev) sequence(3-5) is-84 nt.: ATTTTTTTACCCGTTTTAATCTCTTTAGATTACTGCGTTTCGATATCCCTGATTCCAAATATTGATACAGTCGGTCAACGGTTT 13) The RevCom sequence(5-3) is-84 nt.: TAAAAAAATGGGCAAAATTAGAGAAATCTAATGACGCAAAGCTATAGGGACTAAGGTTTATAACTATGTCAGCCAGTTGCCAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-52 nt.: TTTGGCAACTGGCTGACATAGTTATAAACCTTAGTCCCTATAGCTTTGCGTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-52 nt.: TAAAAAAATGGGCAAAATTAGAGAAATCTAATGACGCAAAGCTATAGGGACT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens, Cyclic di-GMP I type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens, Cyclic di-GMP I type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -13.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -15.56 kcal/mol. The frequency of the MFE structure in the ensemble is 2.54 %. The ensemble diversity is 7.02. The centroid secondary structure in dot-bracket notation with a minimum free energy of -12.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens, Cyclic di-GMP I type switch.

2D_Structure (A) (B)

Multiple alignment of the Cyclic di-GMP I type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP I type switches involved in.

Multi_resistance strains for the Cyclic di-GMP I type switches

RiboSwitch_ID:

CT233381

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RiboSwitch type

Cyclic di-GMP I type switch

Bacteria strain target

Clostridium tetani

Length of Switch in nucleotides

Sequence

CCACGATAAAGGCAAAACTATTGAAAGATAGTGACGCAAAGCTATAGGGTCTGTAAAATGACAGCCAGTTATCGAA

Above is displayed the nucleotide sequence of the Clostridium tetani, Cyclic di-GMP I type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 13 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 15 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 76 nt. 8) CG percentage of the sequence= 39.47% 9) *Melting temperature of the DNA based on the Wallace formula= 72.24oC 10) The entered DNA sequence(5-3) is-76 nt.: CCACGATAAAGGCAAAACTATTGAAAGATAGTGACGCAAAGCTATAGGGTCTGTAAAATGACAGCCAGTTATCGAA 11) The complementary(Com) sequence(3-5) is-76 nt.: GGTGCTATTTCCGTTTTGATAACTTTCTATCACTGCGTTTCGATATCCCAGACATTTTACTGTCGGTCAATAGCTT 12) The reverse(Rev) sequence(3-5) is-76 nt.: AAGCTATTGACCGACAGTAAAATGTCTGGGATATCGAAACGCAGTGATAGAAAGTTATCAAAACGGAAATAGCACC 13) The RevCom sequence(5-3) is-76 nt.: TTCGATAACTGGCTGTCATTTTACAGACCCTATAGCTTTGCGTCACTATCTTTCAATAGTTTTGCCTTTATCGTGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-48 nt.: CCACGATAAAGGCAAAACTATTGAAAGATAGTGACGCAAAGCTATAGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-48 nt.: TTCGATAACTGGCTGTCATTTTACAGACCCTATAGCTTTGCGTCACTA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani, Cyclic di-GMP I type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani, Cyclic di-GMP I type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -15.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -15.96 kcal/mol. The frequency of the MFE structure in the ensemble is 24.65 %. The ensemble diversity is 10.66. The centroid secondary structure in dot-bracket notation with a minimum free energy of -15.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani, Cyclic di-GMP I type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium tetani, Cyclic di-GMP I type switch.

Multiple alignment of the Cyclic di-GMP I type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP I type switches involved in.

Multi_resistance strains for the Cyclic di-GMP I type switches

RiboSwitch_ID:

VC113381

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RiboSwitch type

Cyclic di-GMP I type switch

Bacteria strain target

Vibrio cholerae

Length of Switch in nucleotides

Sequence

TCACGCACAGGGCAAACCATTCGAAAGAGTGGGACGCAAAGCCTCCGGCCTAAACCAGAAGACATGGTAGGTAGCGGGGTTACCGAT

Above is displayed the nucleotide sequence of the Vibrio cholerae, Cyclic di-GMP I type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 26 nt. 4) Thiamine(T) in the sequence= 12 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 87 nt. 8) CG percentage of the sequence= 55.17% 9) *Melting temperature of the DNA based on the Wallace formula= 79.79oC 10) The entered DNA sequence(5-3) is-87 nt.: TCACGCACAGGGCAAACCATTCGAAAGAGTGGGACGCAAAGCCTCCGGCCTAAACCAGAAGACATGGTAGGTAGCGGGGTTACCGAT 11) The complementary(Com) sequence(3-5) is-87 nt.: AGTGCGTGTCCCGTTTGGTAAGCTTTCTCACCCTGCGTTTCGGAGGCCGGATTTGGTCTTCTGTACCATCCATCGCCCCAATGGCTA 12) The reverse(Rev) sequence(3-5) is-87 nt.: TAGCCATTGGGGCGATGGATGGTACAGAAGACCAAATCCGGCCTCCGAAACGCAGGGTGAGAAAGCTTACCAAACGGGACACGCACT 13) The RevCom sequence(5-3) is-87 nt.: ATCGGTAACCCCGCTACCTACCATGTCTTCTGGTTTAGGCCGGAGGCTTTGCGTCCCACTCTTTCGAATGGTTTGCCCTGTGCGTGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-54 nt.: TCACGCACAGGGCAAACCATTCGAAAGAGTGGGACGCAAAGCCTCCGGCCTAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-54 nt.: ATCGGTAACCCCGCTACCTACCATGTCTTCTGGTTTAGGCCGGAGGCTTTGCGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Vibrio cholerae, Cyclic di-GMP I type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Vibrio cholerae, Cyclic di-GMP I type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -26.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -27.15 kcal/mol. The frequency of the MFE structure in the ensemble is 15.43 %. The ensemble diversity is 6.02. The centroid secondary structure in dot-bracket notation with a minimum free energy of -26.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Vibrio cholerae, Cyclic di-GMP I type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Vibrio cholerae, Cyclic di-GMP I type switch.

Multiple alignment of the Cyclic di-GMP I type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP I type switches involved in.

Multi_resistance strains for the Cyclic di-GMP I type switches

RiboSwitch_ID:

CB556381

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RiboSwitch type

Cyclic di-GMP II type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

200

Sequence

TAATTTGTTGGCCGGGTGCACCACTGACTCCTAGTTCTCAAGGTGCCCAAATAAAGAGAACTATTCACAATCTCCAACTTTATA

Above is displayed the nucleotide sequence of the Clostridium botulinum, Cyclic di-GMP II type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 52 nt. 2) Cytosine(C) in the sequence= 60 nt. 3) Guanine(G) in the sequence= 42 nt. 4) Thiamine(T) in the sequence= 46 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 200 nt. 8) CG percentage of the sequence= 51.00% 9) *Melting temperature of the DNA based on the Wallace formula= 82.45oC 10) The entered DNA sequence(5-3) is-200 nt.: TCGGCCGGGCGGCTCCATATACACGTAACCCACCCCCAACCTAACGACGGAGCTACGTGTCTATGGTCTCGCCAACCTTACCTGGCTGCCCGTACCACGTTTCAAATAAATGAAACGAGTATGTTGATACGGGCGTTTCTGCTTGCCAATATATTATGAATATATTGCACAGAAACCGGCTACTCCCCATGAACGGCGCA 11) The complementary(Com) sequence(3-5) is-200 nt.: AGCCGGCCCGCCGAGGTATATGTGCATTGGGTGGGGGTTGGATTGCTGCCTCGATGCACAGATACCAGAGCGGTTGGAATGGACCGACGGGCATGGTGCAAAGTTTATTTACTTTGCTCATACAACTATGCCCGCAAAGACGAACGGTTATATAATACTTATATAACGTGTCTTTGGCCGATGAGGGGTACTTGCCGCGT 12) The reverse(Rev) sequence(3-5) is-200 nt.: ACGCGGCAAGTACCCCTCATCGGCCAAAGACACGTTATATAAGTATTATATAACCGTTCGTCTTTGCGGGCATAGTTGTATGAGCAAAGTAAATAAACTTTGCACCATGCCCGTCGGTCCATTCCAACCGCTCTGGTATCTGTGCATCGAGGCAGCAATCCAACCCCCACCCAATGCACATATACCTCGGCGGGCCGGCT 13) The RevCom sequence(5-3) is-200 nt.: TGCGCCGTTCATGGGGAGTAGCCGGTTTCTGTGCAATATATTCATAATATATTGGCAAGCAGAAACGCCCGTATCAACATACTCGTTTCATTTATTTGAAACGTGGTACGGGCAGCCAGGTAAGGTTGGCGAGACCATAGACACGTAGCTCCGTCGTTAGGTTGGGGGTGGGTTACGTGTATATGGAGCCGCCCGGCCGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-110 nt.: TCGGCCGGGCGGCTCCATATACACGTAACCCACCCCCAACCTAACGACGGAGCTACGTGTCTATGGTCTCGCCAACCTTACCTGGCTGCCCGTACCACGTTTCAAATAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-110 nt.: TGCGCCGTTCATGGGGAGTAGCCGGTTTCTGTGCAATATATTCATAATATATTGGCAAGCAGAAACGCCCGTATCAACATACTCGTTTCATTTATTTGAAACGTGGTACG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum, Cyclic di-GMP II type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum, Cyclic di-GMP II type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -15.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -16.73 kcal/mol. The frequency of the MFE structure in the ensemble is 7.16 %. The ensemble diversity is 16.39. The centroid secondary structure in dot-bracket notation with a minimum free energy of -11.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum, Cyclic di-GMP II type switch.

2D_Structure (A) (B)

Multiple alignment of the Cyclic di-GMP II type switches

Below is presented the sequences alignment of all the Cyclic di-GMP II type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Cyclic di-GMP II type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Cyclic di-GMP-II riboswitches and shorter motifs based on the general one: 1) N{0,6}YN{0,4}GGGGN?GCYN{0,9}RGCTGAGAN{0,13}RACCCN?YN?RRACCTGATCYRGN?TN?ATRCYRGCGN?AGGGAN{0,3}RN{0,13} 2) RRACCTGATCYRG Motifs identified amongst the Cyclic di-GMP-II riboswitches based on the sequences alignment: 1) CAAGGTGCCCA 2) CBAHYWTDWT Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Cyclic di-GMP II type switches involved in.

Multi_resistance strains for the Cyclic di-GMP II type switches

The table displays known human pathogenic bacteria bearing the Cyclic di-GMP II type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

CD111381

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RiboSwitch type

Cyclic di-GMP II type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

Sequence

CAATTTCATAGCCGGTTGCACCACTAACTCAATATGCTCCAAGGTGCCCACATTACAGAACATAAATCAACGTTTCTATTTTATTA

Above is displayed the nucleotide sequence of the Clostridium difficile, Cyclic di-GMP II type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 28 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 10 nt. 4) Thiamine(T) in the sequence= 26 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 86 nt. 8) CG percentage of the sequence= 37.21% 9) *Melting temperature of the DNA based on the Wallace formula= 72.34oC 10) The entered DNA sequence(5-3) is-86 nt.: CAATTTCATAGCCGGTTGCACCACTAACTCAATATGCTCCAAGGTGCCCACATTACAGAACATAAATCAACGTTTCTATTTTATTA 11) The complementary(Com) sequence(3-5) is-86 nt.: GTTAAAGTATCGGCCAACGTGGTGATTGAGTTATACGAGGTTCCACGGGTGTAATGTCTTGTATTTAGTTGCAAAGATAAAATAAT 12) The reverse(Rev) sequence(3-5) is-86 nt.: ATTATTTTATCTTTGCAACTAAATACAAGACATTACACCCGTGGAACCTCGTATAACTCAATCACCACGTTGGCCGATACTTTAAC 13) The RevCom sequence(5-3) is-86 nt.: TAATAAAATAGAAACGTTGATTTATGTTCTGTAATGTGGGCACCTTGGAGCATATTGAGTTAGTGGTGCAACCGGCTATGAAATTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-53 nt.: CAATTTCATAGCCGGTTGCACCACTAACTCAATATGCTCCAAGGTGCCCACAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-53 nt.: TAATAAAATAGAAACGTTGATTTATGTTCTGTAATGTGGGCACCTTGGAGCAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile, Cyclic di-GMP II type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile, Cyclic di-GMP II type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -7.30 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -8.44 kcal/mol. The frequency of the MFE structure in the ensemble is 15.74 %. The ensemble diversity is 8.20. The centroid secondary structure in dot-bracket notation with a minimum free energy of -7.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile, Cyclic di-GMP II type switch.

2D_Structure (A) (B)

Multiple alignment of the Cyclic di-GMP II type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP II type switches involved in.

Multi_resistance strains for the Cyclic di-GMP II type switches

RiboSwitch_ID:

CP32181

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RiboSwitch type

Cyclic di-GMP II type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

Sequence

AAATGTTATAGAAACGTTGATGTATATTCTGTATTTGGGCATCTGGAATATGCTGAGTTAGTGATGCAACCGACTATATTTATA

Above is displayed the nucleotide sequence of the Clostridium perfringens, Cyclic di-GMP II type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 26 nt. 2) Cytosine(C) in the sequence= 9 nt. 3) Guanine(G) in the sequence= 18 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 84 nt. 8) CG percentage of the sequence= 32.14% 9) *Melting temperature of the DNA based on the Wallace formula= 70.07oC 10) The entered DNA sequence(5-3) is-84 nt.: AAATGTTATAGAAACGTTGATGTATATTCTGTATTTGGGCATCTGGAATATGCTGAGTTAGTGATGCAACCGACTATATTTATA 11) The complementary(Com) sequence(3-5) is-84 nt.: TTTACAATATCTTTGCAACTACATATAAGACATAAACCCGTAGACCTTATACGACTCAATCACTACGTTGGCTGATATAAATAT 12) The reverse(Rev) sequence(3-5) is-84 nt.: ATATTTATATCAGCCAACGTAGTGATTGAGTCGTATAAGGTCTACGGGTTTATGTCTTATATGTAGTTGCAAAGATATTGTAAA 13) The RevCom sequence(5-3) is-84 nt.: TATAAATATAGTCGGTTGCATCACTAACTCAGCATATTCCAGATGCCCAAATACAGAATATACATCAACGTTTCTATAACATTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-52 nt.: AAATGTTATAGAAACGTTGATGTATATTCTGTATTTGGGCATCTGGAATATG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-52 nt.: TATAAATATAGTCGGTTGCATCACTAACTCAGCATATTCCAGATGCCCAAAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens, Cyclic di-GMP II type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens, Cyclic di-GMP II type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -12.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -14.62 kcal/mol. The frequency of the MFE structure in the ensemble is 4.46 %. The ensemble diversity is 27.27. The centroid secondary structure in dot-bracket notation with a minimum free energy of -9.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens, Cyclic di-GMP II type switch.

2D_Structure (A) (B)

Multiple alignment of the Cyclic di-GMP II type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP II type switches involved in.

Multi_resistance strains for the Cyclic di-GMP II type switches

RiboSwitch_ID:

CT324841

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RiboSwitch type

Cyclic di-GMP II type switch

Bacteria strain target

Clostridium tetani

Length of Switch in nucleotides

Sequence

ATTTTAAGAGGAAATTTTGAACTATATACTTATTTGGGCACTTTGTATATAGGGAGTTAGTAGTGCAACCGACCTTGATTAAT

Above is displayed the nucleotide sequence of the Clostridium tetani, Cyclic di-GMP II type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 26 nt. 2) Cytosine(C) in the sequence= 9 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 83 nt. 8) CG percentage of the sequence= 31.33% 9) *Melting temperature of the DNA based on the Wallace formula= 69.64oC 10) The entered DNA sequence(5-3) is-83 nt.: ATTTTAAGAGGAAATTTTGAACTATATACTTATTTGGGCACTTTGTATATAGGGAGTTAGTAGTGCAACCGACCTTGATTAAT 11) The complementary(Com) sequence(3-5) is-83 nt.: TAAAATTCTCCTTTAAAACTTGATATATGAATAAACCCGTGAAACATATATCCCTCAATCATCACGTTGGCTGGAACTAATTA 12) The reverse(Rev) sequence(3-5) is-83 nt.: TAATTAGTTCCAGCCAACGTGATGATTGAGGGATATATGTTTCACGGGTTTATTCATATATCAAGTTTTAAAGGAGAATTTTA 13) The RevCom sequence(5-3) is-83 nt.: ATTAATCAAGGTCGGTTGCACTACTAACTCCCTATATACAAAGTGCCCAAATAAGTATATAGTTCAAAATTTCCTCTTAAAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-52 nt.: ATTTTAAGAGGAAATTTTGAACTATATACTTATTTGGGCACTTTGTATATAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-52 nt.: ATTAATCAAGGTCGGTTGCACTACTAACTCCCTATATACAAAGTGCCCAAAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani, Cyclic di-GMP II type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani, Cyclic di-GMP II type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -10.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -12.77 kcal/mol. The frequency of the MFE structure in the ensemble is 3.48 %. The ensemble diversity is 16.56. The centroid secondary structure in dot-bracket notation with a minimum free energy of -10.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani, Cyclic di-GMP II type switch.

2D_Structure (A) (B)

Multiple alignment of the Cyclic di-GMP II type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Cyclic di-GMP II type switches involved in.

Multi_resistance strains for the Cyclic di-GMP II type switches

RiboSwitch_ID:

CP665841

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RiboSwitch type

MOCO type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

195

Sequence

TTTACTTTTGCTTATTCTCCTTCCCAAAATACGTGGAGGCAAAATTCTTTCAAACCTTACCCTGTGGATTACCCCAATTAAACCAATTAACAATTTAAGTTCTTATTAAACTTAATGTTA AATAATTTAGTAATCCAGGCTTAAAAATCATAGAACCTTCTCCTTAGATCTTTAAGCTTGGAGAGTTATACTAAT

Above is displayed the nucleotide sequence of the Clostridium perfringens, MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 65 nt. 2) Cytosine(C) in the sequence= 38 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 71 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 195 nt. 8) CG percentage of the sequence= 30.26% 9) *Melting temperature of the DNA based on the Wallace formula= 73.86oC 10) The entered DNA sequence(5-3) is-195 nt.: TTTACTTTTGCTTATTCTCCTTCCCAAAATACGTGGAGGCAAAATTCTTTCAAACCTTACCCTGTGGATTACCCCAATTAAACCAATTAACAATTTAAGTTCTTATTAAACTTAATGTTAAATAATTTAGTAATCCAGGCTTAAAAATCATAGAACCTTCTCCTTAGATCTTTAAGCTTGGAGAGTTATACTAAT 11) The complementary(Com) sequence(3-5) is-195 nt.: AAATGAAAACGAATAAGAGGAAGGGTTTTATGCACCTCCGTTTTAAGAAAGTTTGGAATGGGACACCTAATGGGGTTAATTTGGTTAATTGTTAAATTCAAGAATAATTTGAATTACAATTTATTAAATCATTAGGTCCGAATTTTTAGTATCTTGGAAGAGGAATCTAGAAATTCGAACCTCTCAATATGATTA 12) The reverse(Rev) sequence(3-5) is-195 nt.: TAATCATATTGAGAGGTTCGAATTTCTAGATTCCTCTTCCAAGATACTAAAAATTCGGACCTAATGATTTAATAAATTGTAATTCAAATTATTCTTGAATTTAACAATTAACCAAATTAACCCCATTAGGTGTCCCATTCCAAACTTTCTTAAAACGGAGGTGCATAAAACCCTTCCTCTTATTCGTTTTCATTT 13) The RevCom sequence(5-3) is-195 nt.: ATTAGTATAACTCTCCAAGCTTAAAGATCTAAGGAGAAGGTTCTATGATTTTTAAGCCTGGATTACTAAATTATTTAACATTAAGTTTAATAAGAACTTAAATTGTTAATTGGTTTAATTGGGGTAATCCACAGGGTAAGGTTTGAAAGAATTTTGCCTCCACGTATTTTGGGAAGGAGAATAAGCAAAAGTAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-108 nt.: TTTACTTTTGCTTATTCTCCTTCCCAAAATACGTGGAGGCAAAATTCTTTCAAACCTTACCCTGTGGATTACCCCAATTAAACCAATTAACAATTTAAGTTCTTATTA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-108 nt.: ATTAGTATAACTCTCCAAGCTTAAAGATCTAAGGAGAAGGTTCTATGATTTTTAAGCCTGGATTACTAAATTATTTAACATTAAGTTTAATAAGAACTTAAATTGTTA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens, MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens, MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -34.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.59 kcal/mol. The frequency of the MFE structure in the ensemble is 0.25 %. The ensemble diversity is 28.97. The centroid secondary structure in dot-bracket notation with a minimum free energy of -28.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens, MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium perfringens, MOCO type switch.

Multiple alignment of the MOCO type switches

Below is presented the sequences alignment of all the MOCO type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the MOCO type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the MOCO riboswitches and shorter motifs based on the general one: 1) N{0,12}CTCCGAGCYN{0,6}YCTAN?RN{0,10}YAN?GRN{0,6}RGCCN{0,16}AGGGTN{0,6}RGAAAYRN{0,5}GCCTCCCN?YN{0,3}TGGAAAGGN?GN{0,16} Motifs identified amongst the MOCO riboswitches based on the sequences alignment: 1) GBNNMABW 2)YBKAW Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

The table displays known human pathogenic bacteria bearing the MOCO type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

EC564441

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RiboSwitch type

MOCO type switch

Bacteria strain target

Clostridium coli

Length of Switch in nucleotides

145

Sequence

ATAACCACTAAACACTCTAGCCTCTGCACCTGGGTCAACTGATACGGTGCTTTGGCCGTGACAATGCTCGTAAAGATTGCCACCAGGGCGAAGGAAGAAATGACTTCGCCTCCCGTATCTGGAAAGGTGTACATGGCTTCACAAC

Above is displayed the nucleotide sequence of the Clostridium coli, MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 40 nt. 2) Cytosine(C) in the sequence= 39 nt. 3) Guanine(G) in the sequence= 34 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 145 nt. 8) CG percentage of the sequence= 50.34% 9) *Melting temperature of the DNA based on the Wallace formula= 80.90oC 10) The entered DNA sequence(5-3) is-145 nt.: ATAACCACTAAACACTCTAGCCTCTGCACCTGGGTCAACTGATACGGTGCTTTGGCCGTGACAATGCTCGTAAAGATTGCCACCAGGGCGAAGGAAGAAATGACTTCGCCTCCCGTATCTGGAAAGGTGTACATGGCTTCACAAC 11) The complementary(Com) sequence(3-5) is-145 nt.: TATTGGTGATTTGTGAGATCGGAGACGTGGACCCAGTTGACTATGCCACGAAACCGGCACTGTTACGAGCATTTCTAACGGTGGTCCCGCTTCCTTCTTTACTGAAGCGGAGGGCATAGACCTTTCCACATGTACCGAAGTGTTG 12) The reverse(Rev) sequence(3-5) is-145 nt.: CAACACTTCGGTACATGTGGAAAGGTCTATGCCCTCCGCTTCAGTAAAGAAGGAAGCGGGACCACCGTTAGAAATGCTCGTAACAGTGCCGGTTTCGTGGCATAGTCAACTGGGTCCACGTCTCCGATCTCACAAATCACCAATA 13) The RevCom sequence(5-3) is-145 nt.: GTTGTGAAGCCATGTACACCTTTCCAGATACGGGAGGCGAAGTCATTTCTTCCTTCGCCCTGGTGGCAATCTTTACGAGCATTGTCACGGCCAAAGCACCGTATCAGTTGACCCAGGTGCAGAGGCTAGAGTGTTTAGTGGTTAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-83 nt.: ATAACCACTAAACACTCTAGCCTCTGCACCTGGGTCAACTGATACGGTGCTTTGGCCGTGACAATGCTCGTAAAGATTGCCAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-83 nt.: GTTGTGAAGCCATGTACACCTTTCCAGATACGGGAGGCGAAGTCATTTCTTCCTTCGCCCTGGTGGCAATCTTTACGAGCATT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium coli, MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium coli, MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -41.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -43.31 kcal/mol. The frequency of the MFE structure in the ensemble is 5.30 %. The ensemble diversity is 25.51. The centroid secondary structure in dot-bracket notation with a minimum free energy of -38.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium coli, MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium coli, MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

ENs64541

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RiboSwitch type

MOCO type switch

Bacteria strain target

Enterobacter sp.

Length of Switch in nucleotides

135

Sequence

GATGAAAACATACACTCTAGCCTTGACGCCTGTGTCACATGATATGGCGCCCTGGCCGTGGCGGTTTCGCCACCAGGGTACAGAAAGAAATGACTGTGCCTCCCGTATCTGGAAAGGTGTACATGGCTTCACAAC

Above is displayed the nucleotide sequence of the Enterobacter sp. , MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 36 nt. 3) Guanine(G) in the sequence= 35 nt. 4) Thiamine(T) in the sequence= 30 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 135 nt. 8) CG percentage of the sequence= 52.59% 9) *Melting temperature of the DNA based on the Wallace formula= 81.48oC 10) The entered DNA sequence(5-3) is-135 nt.: GATGAAAACATACACTCTAGCCTTGACGCCTGTGTCACATGATATGGCGCCCTGGCCGTGGCGGTTTCGCCACCAGGGTACAGAAAGAAATGACTGTGCCTCCCGTATCTGGAAAGGTGTACATGGCTTCACAAC 11) The complementary(Com) sequence(3-5) is-135 nt.: CTACTTTTGTATGTGAGATCGGAACTGCGGACACAGTGTACTATACCGCGGGACCGGCACCGCCAAAGCGGTGGTCCCATGTCTTTCTTTACTGACACGGAGGGCATAGACCTTTCCACATGTACCGAAGTGTTG 12) The reverse(Rev) sequence(3-5) is-135 nt.: CAACACTTCGGTACATGTGGAAAGGTCTATGCCCTCCGTGTCAGTAAAGAAAGACATGGGACCACCGCTTTGGCGGTGCCGGTCCCGCGGTATAGTACACTGTGTCCGCAGTTCCGATCTCACATACAAAAGTAG 13) The RevCom sequence(5-3) is-135 nt.: GTTGTGAAGCCATGTACACCTTTCCAGATACGGGAGGCACAGTCATTTCTTTCTGTACCCTGGTGGCGAAACCGCCACGGCCAGGGCGCCATATCATGTGACACAGGCGTCAAGGCTAGAGTGTATGTTTTCATC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-78 nt.: GATGAAAACATACACTCTAGCCTTGACGCCTGTGTCACATGATATGGCGCCCTGGCCGTGGCGGTTTCGCCACCAGGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-78 nt.: GTTGTGAAGCCATGTACACCTTTCCAGATACGGGAGGCACAGTCATTTCTTTCTGTACCCTGGTGGCGAAACCGCCAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterobacter sp. , MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterobacter sp. , MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -45.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -47.90 kcal/mol. The frequency of the MFE structure in the ensemble is 3.89 %. The ensemble diversity is 30.40. The centroid secondary structure in dot-bracket notation with a minimum free energy of -39.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterobacter sp. , MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterobacter sp. , MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

HI64941

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RiboSwitch type

MOCO type switch

Bacteria strain target

Haemophilus influenzae

Length of Switch in nucleotides

141

Sequence

AATGGATTGCATTTTACACCTTTCTAAATACGGAGAGGATAAACCGTTTCCAGCGTATCCCTGAATAACGTAGCGCGTTATTGGCTTGCCACCGTATTTCTATGAAACTTAGGCTAAACAAGCTCGGAGTTATGCGTTAAA

Above is displayed the nucleotide sequence of the Haemophilus influenzae, MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 41 nt. 2) Cytosine(C) in the sequence= 29 nt. 3) Guanine(G) in the sequence= 29 nt. 4) Thiamine(T) in the sequence= 42 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 141 nt. 8) CG percentage of the sequence= 41.13% 9) *Melting temperature of the DNA based on the Wallace formula= 77.00oC 10) The entered DNA sequence(5-3) is-141 nt.: AATGGATTGCATTTTACACCTTTCTAAATACGGAGAGGATAAACCGTTTCCAGCGTATCCCTGAATAACGTAGCGCGTTATTGGCTTGCCACCGTATTTCTATGAAACTTAGGCTAAACAAGCTCGGAGTTATGCGTTAAA 11) The complementary(Com) sequence(3-5) is-141 nt.: TTACCTAACGTAAAATGTGGAAAGATTTATGCCTCTCCTATTTGGCAAAGGTCGCATAGGGACTTATTGCATCGCGCAATAACCGAACGGTGGCATAAAGATACTTTGAATCCGATTTGTTCGAGCCTCAATACGCAATTT 12) The reverse(Rev) sequence(3-5) is-141 nt.: AAATTGCGTATTGAGGCTCGAACAAATCGGATTCAAAGTATCTTTATGCCACCGTTCGGTTATTGCGCGATGCAATAAGTCCCTATGCGACCTTTGCCAAATAGGAGAGGCATAAATCTTTCCACATTTTACGTTAGGTAA 13) The RevCom sequence(5-3) is-141 nt.: TTTAACGCATAACTCCGAGCTTGTTTAGCCTAAGTTTCATAGAAATACGGTGGCAAGCCAATAACGCGCTACGTTATTCAGGGATACGCTGGAAACGGTTTATCCTCTCCGTATTTAGAAAGGTGTAAAATGCAATCCATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-81 nt.: AATGGATTGCATTTTACACCTTTCTAAATACGGAGAGGATAAACCGTTTCCAGCGTATCCCTGAATAACGTAGCGCGTTAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-81 nt.: TTTAACGCATAACTCCGAGCTTGTTTAGCCTAAGTTTCATAGAAATACGGTGGCAAGCCAATAACGCGCTACGTTATTCAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Haemophilus influenzae, MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Haemophilus influenzae, MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -30.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -33.32 kcal/mol. The frequency of the MFE structure in the ensemble is 1.20 %. The ensemble diversity is 35.14. The centroid secondary structure in dot-bracket notation with a minimum free energy of -21.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Haemophilus influenzae, MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Haemophilus influenzae, MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

KP11651

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RiboSwitch type

MOCO type switch

Bacteria strain target

Klebsiella pneumoniae

Length of Switch in nucleotides

139

Sequence

ATAACCTGTTAACACTCTAGCCTCTTCGCCTGTGTCAAAAGATATGGCGATTTGGCCGCGACGCCGCCGGTTGTCGCCAGGGCGTGGAAAGAAATGACCGCGTCTCCCGTATTTGGAAAGGTGTATATGGCCTCACAGC

Above is displayed the nucleotide sequence of the Klebsiella pneumoniae, MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 31 nt. 2) Cytosine(C) in the sequence= 37 nt. 3) Guanine(G) in the sequence= 38 nt. 4) Thiamine(T) in the sequence= 33 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 139 nt. 8) CG percentage of the sequence= 53.96% 9) *Melting temperature of the DNA based on the Wallace formula= 82.18oC 10) The entered DNA sequence(5-3) is-139 nt.: ATAACCTGTTAACACTCTAGCCTCTTCGCCTGTGTCAAAAGATATGGCGATTTGGCCGCGACGCCGCCGGTTGTCGCCAGGGCGTGGAAAGAAATGACCGCGTCTCCCGTATTTGGAAAGGTGTATATGGCCTCACAGC 11) The complementary(Com) sequence(3-5) is-139 nt.: TATTGGACAATTGTGAGATCGGAGAAGCGGACACAGTTTTCTATACCGCTAAACCGGCGCTGCGGCGGCCAACAGCGGTCCCGCACCTTTCTTTACTGGCGCAGAGGGCATAAACCTTTCCACATATACCGGAGTGTCG 12) The reverse(Rev) sequence(3-5) is-139 nt.: CGACACTCCGGTATATGTGGAAAGGTTTATGCCCTCTGCGCCAGTAAAGAAAGGTGCGGGACCGCTGTTGGCCGCCGCAGCGCCGGTTTAGCGGTATAGAAAACTGTGTCCGCTTCTCCGATCTCACAATTGTCCAATA 13) The RevCom sequence(5-3) is-139 nt.: GCTGTGAGGCCATATACACCTTTCCAAATACGGGAGACGCGGTCATTTCTTTCCACGCCCTGGCGACAACCGGCGGCGTCGCGGCCAAATCGCCATATCTTTTGACACAGGCGAAGAGGCTAGAGTGTTAACAGGTTAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-80 nt.: ATAACCTGTTAACACTCTAGCCTCTTCGCCTGTGTCAAAAGATATGGCGATTTGGCCGCGACGCCGCCGGTTGTCGCCAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-80 nt.: GCTGTGAGGCCATATACACCTTTCCAAATACGGGAGACGCGGTCATTTCTTTCCACGCCCTGGCGACAACCGGCGGCGTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Klebsiella pneumoniae, MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Klebsiella pneumoniae, MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -45.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -47.21 kcal/mol. The frequency of the MFE structure in the ensemble is 6.26 %. The ensemble diversity is 15.51. The centroid secondary structure in dot-bracket notation with a minimum free energy of -38.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Klebsiella pneumoniae, MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Klebsiella pneumoniae, MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

SE917651

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RiboSwitch type

MOCO type switch

Bacteria strain target

Salmonella enterica

Length of Switch in nucleotides

144

Sequence

GTTGTGAAGCCATGTACACCTTTCCAAATACGGGAGGCGGAGTCATTTCTTCCTGCGCCCTGGTGGCAAACGCTGAACGTTGTCACGGCCAAAACACCGTATCAAAATGACCCAGGTGCAGAGGCTAGAGTGTTTACTGTGGTT

Above is displayed the nucleotide sequence of the Salmonella enterica, MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 35 nt. 2) Cytosine(C) in the sequence= 35 nt. 3) Guanine(G) in the sequence= 39 nt. 4) Thiamine(T) in the sequence= 35 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 144 nt. 8) CG percentage of the sequence= 51.39% 9) *Melting temperature of the DNA based on the Wallace formula= 81.30oC 10) The entered DNA sequence(5-3) is-144 nt.: GTTGTGAAGCCATGTACACCTTTCCAAATACGGGAGGCGGAGTCATTTCTTCCTGCGCCCTGGTGGCAAACGCTGAACGTTGTCACGGCCAAAACACCGTATCAAAATGACCCAGGTGCAGAGGCTAGAGTGTTTACTGTGGTT 11) The complementary(Com) sequence(3-5) is-144 nt.: CAACACTTCGGTACATGTGGAAAGGTTTATGCCCTCCGCCTCAGTAAAGAAGGACGCGGGACCACCGTTTGCGACTTGCAACAGTGCCGGTTTTGTGGCATAGTTTTACTGGGTCCACGTCTCCGATCTCACAAATGACACCAA 12) The reverse(Rev) sequence(3-5) is-144 nt.: TTGGTGTCATTTGTGAGATCGGAGACGTGGACCCAGTAAAACTATGCCACAAAACCGGCACTGTTGCAAGTCGCAAACGGTGGTCCCGCGTCCTTCTTTACTGAGGCGGAGGGCATAAACCTTTCCACATGTACCGAAGTGTTG 13) The RevCom sequence(5-3) is-144 nt.: AACCACAGTAAACACTCTAGCCTCTGCACCTGGGTCATTTTGATACGGTGTTTTGGCCGTGACAACGTTCAGCGTTTGCCACCAGGGCGCAGGAAGAAATGACTCCGCCTCCCGTATTTGGAAAGGTGTACATGGCTTCACAAC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-82 nt.: GTTGTGAAGCCATGTACACCTTTCCAAATACGGGAGGCGGAGTCATTTCTTCCTGCGCCCTGGTGGCAAACGCTGAACGTTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-82 nt.: AACCACAGTAAACACTCTAGCCTCTGCACCTGGGTCATTTTGATACGGTGTTTTGGCCGTGACAACGTTCAGCGTTTGCCAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella enterica, MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella enterica, MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -40.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -43.72 kcal/mol. The frequency of the MFE structure in the ensemble is 0.28 %. The ensemble diversity is 45.70. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella enterica, MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella enterica, MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

ST849051

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RiboSwitch type

MOCO type switch

Bacteria strain target

Salmonella typhi

Length of Switch in nucleotides

145

Sequence

AACCACAGTAAACACTCTAGCCTCTGCACCTGGGTCATTTTTGATACGGTGCTTTGGCCGTGACAACGTTTAACGTTTGCCACCAGGGCGCAGGAAGAAATGACTCCGCCTCCCGTATTTGGAAAGGTGTACATGGCTTCACAAC

Above is displayed the nucleotide sequence of the Salmonella typhi , MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 36 nt. 2) Cytosine(C) in the sequence= 39 nt. 3) Guanine(G) in the sequence= 34 nt. 4) Thiamine(T) in the sequence= 36 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 145 nt. 8) CG percentage of the sequence= 50.34% 9) *Melting temperature of the DNA based on the Wallace formula= 80.90oC 10) The entered DNA sequence(5-3) is-145 nt.: AACCACAGTAAACACTCTAGCCTCTGCACCTGGGTCATTTTTGATACGGTGCTTTGGCCGTGACAACGTTTAACGTTTGCCACCAGGGCGCAGGAAGAAATGACTCCGCCTCCCGTATTTGGAAAGGTGTACATGGCTTCACAAC 11) The complementary(Com) sequence(3-5) is-145 nt.: TTGGTGTCATTTGTGAGATCGGAGACGTGGACCCAGTAAAAACTATGCCACGAAACCGGCACTGTTGCAAATTGCAAACGGTGGTCCCGCGTCCTTCTTTACTGAGGCGGAGGGCATAAACCTTTCCACATGTACCGAAGTGTTG 12) The reverse(Rev) sequence(3-5) is-145 nt.: CAACACTTCGGTACATGTGGAAAGGTTTATGCCCTCCGCCTCAGTAAAGAAGGACGCGGGACCACCGTTTGCAATTTGCAACAGTGCCGGTTTCGTGGCATAGTTTTTACTGGGTCCACGTCTCCGATCTCACAAATGACACCAA 13) The RevCom sequence(5-3) is-145 nt.: GTTGTGAAGCCATGTACACCTTTCCAAATACGGGAGGCGGAGTCATTTCTTCCTGCGCCCTGGTGGCAAACGTTAAACGTTGTCACGGCCAAAGCACCGTATCAAAAATGACCCAGGTGCAGAGGCTAGAGTGTTTACTGTGGTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-83 nt.: AACCACAGTAAACACTCTAGCCTCTGCACCTGGGTCATTTTTGATACGGTGCTTTGGCCGTGACAACGTTTAACGTTTGCCAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-83 nt.: GTTGTGAAGCCATGTACACCTTTCCAAATACGGGAGGCGGAGTCATTTCTTCCTGCGCCCTGGTGGCAAACGTTAAACGTTGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella typhi , MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella typhi , MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -43.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -45.43 kcal/mol. The frequency of the MFE structure in the ensemble is 2.27 %. The ensemble diversity is 11.22. The centroid secondary structure in dot-bracket notation with a minimum free energy of -42.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella typhi , MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella typhi , MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

VC986051

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RiboSwitch type

MOCO type switch

Bacteria strain target

Vibrio cholerae

Length of Switch in nucleotides

140

Sequence

GCTTGGCCTTAACTCCGAGCTTACCGCGCTAAGTTTAAACCTTTAAATATGCGTTGTAAGCCAGTGACCGCTTGTCACAAGGGCAGAATTGGAAATGATTTTGCCTCCCGTATTTGGAAAGGTGTTCTGTGGCGCAACAA

Above is displayed the nucleotide sequence of the Vibrio cholerae , MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 35 nt. 2) Cytosine(C) in the sequence= 31 nt. 3) Guanine(G) in the sequence= 34 nt. 4) Thiamine(T) in the sequence= 40 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 140 nt. 8) CG percentage of the sequence= 46.43% 9) *Melting temperature of the DNA based on the Wallace formula= 79.13oC 10) The entered DNA sequence(5-3) is-140 nt.: GCTTGGCCTTAACTCCGAGCTTACCGCGCTAAGTTTAAACCTTTAAATATGCGTTGTAAGCCAGTGACCGCTTGTCACAAGGGCAGAATTGGAAATGATTTTGCCTCCCGTATTTGGAAAGGTGTTCTGTGGCGCAACAA 11) The complementary(Com) sequence(3-5) is-140 nt.: CGAACCGGAATTGAGGCTCGAATGGCGCGATTCAAATTTGGAAATTTATACGCAACATTCGGTCACTGGCGAACAGTGTTCCCGTCTTAACCTTTACTAAAACGGAGGGCATAAACCTTTCCACAAGACACCGCGTTGTT 12) The reverse(Rev) sequence(3-5) is-140 nt.: AACAACGCGGTGTCTTGTGGAAAGGTTTATGCCCTCCGTTTTAGTAAAGGTTAAGACGGGAACACTGTTCGCCAGTGACCGAATGTTGCGTATAAATTTCCAAATTTGAATCGCGCCATTCGAGCCTCAATTCCGGTTCG 13) The RevCom sequence(5-3) is-140 nt.: TTGTTGCGCCACAGAACACCTTTCCAAATACGGGAGGCAAAATCATTTCCAATTCTGCCCTTGTGACAAGCGGTCACTGGCTTACAACGCATATTTAAAGGTTTAAACTTAGCGCGGTAAGCTCGGAGTTAAGGCCAAGC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-80 nt.: GCTTGGCCTTAACTCCGAGCTTACCGCGCTAAGTTTAAACCTTTAAATATGCGTTGTAAGCCAGTGACCGCTTGTCACAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-80 nt.: TTGTTGCGCCACAGAACACCTTTCCAAATACGGGAGGCAAAATCATTTCCAATTCTGCCCTTGTGACAAGCGGTCACTGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Vibrio cholerae , MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Vibrio cholerae , MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -43.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -45.73 kcal/mol. The frequency of the MFE structure in the ensemble is 5.14 %. The ensemble diversity is 35.27. The centroid secondary structure in dot-bracket notation with a minimum free energy of -37.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Vibrio cholerae , MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Vibrio cholerae , MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

YP554351

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RiboSwitch type

MOCO type switch

Bacteria strain target

Yersinia pestis

Length of Switch in nucleotides

148

Sequence

CGCTGAACATAAACTCCTAGCCTTAGCGTCTACGTTGTCTTTTTTGTATTGGCAATATGATGTTCTGGCCGTGGCCTTAAGCCACCAGGGTGCAAGGTAGAAATGCCTGCATCTCCCGTATTTGGAAAGGTGTTATGGTACAACTCAC

Above is displayed the nucleotide sequence of the Yersinia pestis , MOCO type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 34 nt. 3) Guanine(G) in the sequence= 35 nt. 4) Thiamine(T) in the sequence= 45 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 148 nt. 8) CG percentage of the sequence= 46.62% 9) *Melting temperature of the DNA based on the Wallace formula= 79.47oC 10) The entered DNA sequence(5-3) is-148 nt.: CGCTGAACATAAACTCCTAGCCTTAGCGTCTACGTTGTCTTTTTTGTATTGGCAATATGATGTTCTGGCCGTGGCCTTAAGCCACCAGGGTGCAAGGTAGAAATGCCTGCATCTCCCGTATTTGGAAAGGTGTTATGGTACAACTCAC 11) The complementary(Com) sequence(3-5) is-148 nt.: GCGACTTGTATTTGAGGATCGGAATCGCAGATGCAACAGAAAAAACATAACCGTTATACTACAAGACCGGCACCGGAATTCGGTGGTCCCACGTTCCATCTTTACGGACGTAGAGGGCATAAACCTTTCCACAATACCATGTTGAGTG 12) The reverse(Rev) sequence(3-5) is-148 nt.: CACTCAACATGGTATTGTGGAAAGGTTTATGCCCTCTACGTCCGTAAAGATGGAACGTGGGACCACCGAATTCCGGTGCCGGTCTTGTAGTATAACGGTTATGTTTTTTCTGTTGCATCTGCGATTCCGATCCTCAAATACAAGTCGC 13) The RevCom sequence(5-3) is-148 nt.: GTGAGTTGTACCATAACACCTTTCCAAATACGGGAGATGCAGGCATTTCTACCTTGCACCCTGGTGGCTTAAGGCCACGGCCAGAACATCATATTGCCAATACAAAAAAGACAACGTAGACGCTAAGGCTAGGAGTTTATGTTCAGCG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-84 nt.: CGCTGAACATAAACTCCTAGCCTTAGCGTCTACGTTGTCTTTTTTGTATTGGCAATATGATGTTCTGGCCGTGGCCTTAAGCCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-84 nt.: GTGAGTTGTACCATAACACCTTTCCAAATACGGGAGATGCAGGCATTTCTACCTTGCACCCTGGTGGCTTAAGGCCACGGCCAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Yersinia pestis , MOCO type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Yersinia pestis , MOCO type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -45.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -47.54 kcal/mol. The frequency of the MFE structure in the ensemble is 1.91 %. The ensemble diversity is 9.77. The centroid secondary structure in dot-bracket notation with a minimum free energy of -42.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Yersinia pestis , MOCO type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Yersinia pestis , MOCO type switch.

Multiple alignment of the MOCO type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the MOCO type switches involved in.

Multi_resistance strains for the MOCO type switches

RiboSwitch_ID:

BA7784351

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

Sequence

AATAACGTGGTTCGAAACCATCCCACGTAAAAAAACTAAGGAGAT

Above is displayed the nucleotide sequence of the Bacillus anthracis , PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 9 nt. 3) Guanine(G) in the sequence= 8 nt. 4) Thiamine(T) in the sequence= 8 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 37.78% 9) *Melting temperature of the DNA based on the Wallace formula= 65.45oC 10) The entered DNA sequence(5-3) is-45 nt.: AATAACGTGGTTCGAAACCATCCCACGTAAAAAAACTAAGGAGAT 11) The complementary(Com) sequence(3-5) is-45 nt.: TTATTGCACCAAGCTTTGGTAGGGTGCATTTTTTTGATTCCTCTA 12) The reverse(Rev) sequence(3-5) is-45 nt.: TAGAGGAATCAAAAAAATGCACCCTACCAAAGCTTGGTGCAATAA 13) The RevCom sequence(5-3) is-45 nt.: ATCTCCTTAGTTTTTTTACGTGGGATGGTTTCGAACCACGTTATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: AATAACGTGGTTCGAAACCATCCCACGTAAAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: ATCTCCTTAGTTTTTTTACGTGGGATGGTTTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis , PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis , PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -7.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -7.38 kcal/mol. The frequency of the MFE structure in the ensemble is 53.77 %. The ensemble diversity is 2.60. The centroid secondary structure in dot-bracket notation with a minimum free energy of -7.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis , PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis , PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Below is presented the sequences alignment of all the PreQ1 type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the PreQ1 type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the PreQ1 riboswitches and shorter motifs based on the general one: 1) N?YN?RN{0,2}GN?GGTTCRN?RRN?CN?TCCCN?CN{0,3}AAAAAACTARGN?RN{0,3} Motifs identified amongst the PreQ1 riboswitches based on the sequences alignment: 1) WDGTT 2) AACYW Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

The table displays known human pathogenic bacteria bearing the PreQ1 type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

CB2734353

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

Sequence

AATTGCCTAGTTTTTTATAGAGGGATGGTCTTCGAACCTCTCCCAC

Above is displayed the nucleotide sequence of the Clostridium botulinum, PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 10 nt. 2) Cytosine(C) in the sequence= 11 nt. 3) Guanine(G) in the sequence= 9 nt. 4) Thiamine(T) in the sequence= 16 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 46 nt. 8) CG percentage of the sequence= 43.48% 9) *Melting temperature of the DNA based on the Wallace formula= 68.11oC 10) The entered DNA sequence(5-3) is-46 nt.: AATTGCCTAGTTTTTTATAGAGGGATGGTCTTCGAACCTCTCCCAC 11) The complementary(Com) sequence(3-5) is-46 nt.: TTAACGGATCAAAAAATATCTCCCTACCAGAAGCTTGGAGAGGGTG 12) The reverse(Rev) sequence(3-5) is-46 nt.: CACCCTCTCCAAGCTTCTGGTAGGGAGATATTTTTTGATCCGTTAA 13) The RevCom sequence(5-3) is-46 nt.: GTGGGAGAGGTTCGAAGACCATCCCTCTATAAAAAACTAGGCAATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: AATTGCCTAGTTTTTTATAGAGGGATGGTCTTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: GTGGGAGAGGTTCGAAGACCATCCCTCTATAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum, PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum, PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -9.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -9.61 kcal/mol. The frequency of the MFE structure in the ensemble is 51.31 %. The ensemble diversity is 2.81. The centroid secondary structure in dot-bracket notation with a minimum free energy of -9.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum, PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum, PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

CD253353

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

Sequence

TCTGTACTTGTTCGAGAACTCCAAGTATAAAAAACTAAGGAATT

Above is displayed the nucleotide sequence of the Clostridium difficile, PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 17 nt. 2) Cytosine(C) in the sequence= 7 nt. 3) Guanine(G) in the sequence= 7 nt. 4) Thiamine(T) in the sequence= 13 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 44 nt. 8) CG percentage of the sequence= 31.82% 9) *Melting temperature of the DNA based on the Wallace formula= 62.66oC 10) The entered DNA sequence(5-3) is-44 nt.: TCTGTACTTGTTCGAGAACTCCAAGTATAAAAAACTAAGGAATT 11) The complementary(Com) sequence(3-5) is-44 nt.: AGACATGAACAAGCTCTTGAGGTTCATATTTTTTGATTCCTTAA 12) The reverse(Rev) sequence(3-5) is-44 nt.: TTAAGGAATCAAAAAATATGAACCTCAAGAGCTTGTTCATGTCT 13) The RevCom sequence(5-3) is-44 nt.: AATTCCTTAGTTTTTTATACTTGGAGTTCTCGAACAAGTACAGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-32 nt.: TCTGTACTTGTTCGAGAACTCCAAGTATAAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-32 nt.: AATTCCTTAGTTTTTTATACTTGGAGTTCTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile, PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile, PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -0 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -0 kcal/mol. The frequency of the MFE structure in the ensemble is 0 %. The ensemble diversity is 0. The centroid secondary structure in dot-bracket notation with a minimum free energy of -0.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile, PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium difficile, PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

CP447753

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

Sequence

CAGCCCTTAGTTTTTTATAGAGGGATGGTTACGAACCTCTACCAA

Above is displayed the nucleotide sequence of the Clostridium perfringens, PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 12 nt. 2) Cytosine(C) in the sequence= 10 nt. 3) Guanine(G) in the sequence= 9 nt. 4) Thiamine(T) in the sequence= 14 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 42.22% 9) *Melting temperature of the DNA based on the Wallace formula= 67.27oC 10) The entered DNA sequence(5-3) is-45 nt.: CAGCCCTTAGTTTTTTATAGAGGGATGGTTACGAACCTCTACCAA 11) The complementary(Com) sequence(3-5) is-45 nt.: GTCGGGAATCAAAAAATATCTCCCTACCAATGCTTGGAGATGGTT 12) The reverse(Rev) sequence(3-5) is-45 nt.: AACCATCTCCAAGCATTGGTAGGGAGATATTTTTTGATTCCCGAC 13) The RevCom sequence(5-3) is-45 nt.: TTGGTAGAGGTTCGTAACCATCCCTCTATAAAAAACTAAGGGCTG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: CAGCCCTTAGTTTTTTATAGAGGGATGGTTACG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: TTGGTAGAGGTTCGTAACCATCCCTCTATAAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens, PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens, PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -5.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -6.37 kcal/mol. The frequency of the MFE structure in the ensemble is 46.77 %. The ensemble diversity is 1.75. The centroid secondary structure in dot-bracket notation with a minimum free energy of -5.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens, PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium perfringens, PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

CF479593

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Enterococcus faecalis

Length of Switch in nucleotides

Sequence

CTCGGACTGGTTCGGAAACTTCCCAGAATAAAAAACTAAGTATCT

Above is displayed the nucleotide sequence of the Enterococcus faecalis, PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 16 nt. 2) Cytosine(C) in the sequence= 10 nt. 3) Guanine(G) in the sequence= 8 nt. 4) Thiamine(T) in the sequence= 11 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 40.00% 9) *Melting temperature of the DNA based on the Wallace formula= 66.36oC 10) The entered DNA sequence(5-3) is-45 nt.: CTCGGACTGGTTCGGAAACTTCCCAGAATAAAAAACTAAGTATCT 11) The complementary(Com) sequence(3-5) is-45 nt.: GAGCCTGACCAAGCCTTTGAAGGGTCTTATTTTTTGATTCATAGA 12) The reverse(Rev) sequence(3-5) is-45 nt.: TCTATGAATCAAAAAATAAGACCCTTCAAAGGCTTGGTCAGGCTC 13) The RevCom sequence(5-3) is-45 nt.: AGATACTTAGTTTTTTATTCTGGGAAGTTTCCGAACCAGTCCGAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: CTCGGACTGGTTCGGAAACTTCCCAGAATAAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: AGATACTTAGTTTTTTATTCTGGGAAGTTTCCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecalis, PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecalis, PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -3.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -4.70 kcal/mol. The frequency of the MFE structure in the ensemble is 19.66 %. The ensemble diversity is 10.85. The centroid secondary structure in dot-bracket notation with a minimum free energy of -0.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecalis, PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecalis, PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

CF471193

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Enterococcus faecium

Length of Switch in nucleotides

Sequence

CTTGGACTGGTTCGGAAACTTCCCAGAATAAAAAACTAAGTATCT

Above is displayed the nucleotide sequence of the Enterococcus faecium , PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 16 nt. 2) Cytosine(C) in the sequence= 9 nt. 3) Guanine(G) in the sequence= 8 nt. 4) Thiamine(T) in the sequence= 12 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 37.78% 9) *Melting temperature of the DNA based on the Wallace formula= 65.45oC 10) The entered DNA sequence(5-3) is-45 nt.: CTTGGACTGGTTCGGAAACTTCCCAGAATAAAAAACTAAGTATCT 11) The complementary(Com) sequence(3-5) is-45 nt.: GAACCTGACCAAGCCTTTGAAGGGTCTTATTTTTTGATTCATAGA 12) The reverse(Rev) sequence(3-5) is-45 nt.: TCTATGAATCAAAAAATAAGACCCTTCAAAGGCTTGGTCAGGTTC 13) The RevCom sequence(5-3) is-45 nt.: AGATACTTAGTTTTTTATTCTGGGAAGTTTCCGAACCAGTCCAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: CTTGGACTGGTTCGGAAACTTCCCAGAATAAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: AGATACTTAGTTTTTTATTCTGGGAAGTTTCCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecium , PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecium , PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -5.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -6.10 kcal/mol. The frequency of the MFE structure in the ensemble is 44.12 %. The ensemble diversity is 6.18. The centroid secondary structure in dot-bracket notation with a minimum free energy of -5.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecium , PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecium , PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

HI981193

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Haemophilus influenzae

Length of Switch in nucleotides

Sequence

TTTTACCTAGTTTTTTATTGTAGGAGGTTTGCGAACTACGGGGGG

Above is displayed the nucleotide sequence of the Haemophilus influenzae , PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 8 nt. 2) Cytosine(C) in the sequence= 5 nt. 3) Guanine(G) in the sequence= 14 nt. 4) Thiamine(T) in the sequence= 18 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 42.22% 9) *Melting temperature of the DNA based on the Wallace formula= 67.27oC 10) The entered DNA sequence(5-3) is-45 nt.: TTTTACCTAGTTTTTTATTGTAGGAGGTTTGCGAACTACGGGGGG 11) The complementary(Com) sequence(3-5) is-45 nt.: AAAATGGATCAAAAAATAACATCCTCCAAACGCTTGATGCCCCCC 12) The reverse(Rev) sequence(3-5) is-45 nt.: GGGGGGCATCAAGCGTTTGGAGGATGTTATTTTTTGATCCATTTT 13) The RevCom sequence(5-3) is-45 nt.: CCCCCCGTAGTTCGCAAACCTCCTACAATAAAAAACTAGGTAAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: TTTTACCTAGTTTTTTATTGTAGGAGGTTTGCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: CCCCCCGTAGTTCGCAAACCTCCTACAATAAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Haemophilus influenzae , PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Haemophilus influenzae , PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -5.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -6.80 kcal/mol. The frequency of the MFE structure in the ensemble is 5.37 %. The ensemble diversity is 11.79. The centroid secondary structure in dot-bracket notation with a minimum free energy of -2.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Haemophilus influenzae , PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Haemophilus influenzae , PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

LM961243

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

Sequence

CCACACGTGGTTCATTCATACCATCCCACGTAAAAAAACTAGGAGGAA

Above is displayed the nucleotide sequence of the Listeria monocytogenes , PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 18 nt. 2) Cytosine(C) in the sequence= 13 nt. 3) Guanine(G) in the sequence= 8 nt. 4) Thiamine(T) in the sequence= 9 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 48 nt. 8) CG percentage of the sequence= 43.75% 9) *Melting temperature of the DNA based on the Wallace formula= 68.83oC 10) The entered DNA sequence(5-3) is-48 nt.: CCACACGTGGTTCATTCATACCATCCCACGTAAAAAAACTAGGAGGAA 11) The complementary(Com) sequence(3-5) is-48 nt.: GGTGTGCACCAAGTAAGTATGGTAGGGTGCATTTTTTTGATCCTCCTT 12) The reverse(Rev) sequence(3-5) is-48 nt.: AAGGAGGATCAAAAAAATGCACCCTACCATACTTACTTGGTGCACACC 13) The RevCom sequence(5-3) is-48 nt.: TTCCTCCTAGTTTTTTTACGTGGGATGGTATGAATGAACCACGTGTGG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-34 nt.: CCACACGTGGTTCATTCATACCATCCCACGTAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-34 nt.: TTCCTCCTAGTTTTTTTACGTGGGATGGTATGAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes , PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes , PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -6.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -6.99 kcal/mol. The frequency of the MFE structure in the ensemble is 53.41 %. The ensemble diversity is 6.79. The centroid secondary structure in dot-bracket notation with a minimum free energy of -6.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes , PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes , PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

NG643486

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Neisseria gonorrhoeae

Length of Switch in nucleotides

Sequence

CGCCCCGTGGTTCGAAAACCTCCCACACTAAAAAACTAAGGAAAC

Above is displayed the nucleotide sequence of the Neisseria gonorrhoeae, PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 17 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 7 nt. 4) Thiamine(T) in the sequence= 6 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 48.89% 9) *Melting temperature of the DNA based on the Wallace formula= 70.00oC 10) The entered DNA sequence(5-3) is-45 nt.: CGCCCCGTGGTTCGAAAACCTCCCACACTAAAAAACTAAGGAAAC 11) The complementary(Com) sequence(3-5) is-45 nt.: GCGGGGCACCAAGCTTTTGGAGGGTGTGATTTTTTGATTCCTTTG 12) The reverse(Rev) sequence(3-5) is-45 nt.: CAAAGGAATCAAAAAATCACACCCTCCAAAAGCTTGGTGCCCCGC 13) The RevCom sequence(5-3) is-45 nt.: GTTTCCTTAGTTTTTTAGTGTGGGAGGTTTTCGAACCACGGGGCG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: CGCCCCGTGGTTCGAAAACCTCCCACACTAAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: GTTTCCTTAGTTTTTTAGTGTGGGAGGTTTTCG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Neisseria gonorrhoeae, PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Neisseria gonorrhoeae, PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -3.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -4.16 kcal/mol. The frequency of the MFE structure in the ensemble is 29.17 %. The ensemble diversity is 7.25. The centroid secondary structure in dot-bracket notation with a minimum free energy of -3.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Neisseria gonorrhoeae, PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Neisseria gonorrhoeae, PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

NM643667

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Neisseria meningitidis

Length of Switch in nucleotides

Sequence

GTTTCCTTAGTTTTTTAATGTGGGAGGTTTTCGAACCACGGGCGG

Above is displayed the nucleotide sequence of the Neisseria meningitidis, PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 7 nt. 2) Cytosine(C) in the sequence= 7 nt. 3) Guanine(G) in the sequence= 14 nt. 4) Thiamine(T) in the sequence= 17 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 46.67% 9) *Melting temperature of the DNA based on the Wallace formula= 69.09oC 10) The entered DNA sequence(5-3) is-45 nt.: GTTTCCTTAGTTTTTTAATGTGGGAGGTTTTCGAACCACGGGCGG 11) The complementary(Com) sequence(3-5) is-45 nt.: CAAAGGAATCAAAAAATTACACCCTCCAAAAGCTTGGTGCCCGCC 12) The reverse(Rev) sequence(3-5) is-45 nt.: GGCGGGCACCAAGCTTTTGGAGGGTGTAATTTTTTGATTCCTTTG 13) The RevCom sequence(5-3) is-45 nt.: CCGCCCGTGGTTCGAAAACCTCCCACATTAAAAAACTAAGGAAAC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: GTTTCCTTAGTTTTTTAATGTGGGAGGTTTTCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: CCGCCCGTGGTTCGAAAACCTCCCACATTAAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Neisseria meningitidis, PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Neisseria meningitidis, PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -7.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -7.73 kcal/mol. The frequency of the MFE structure in the ensemble is 30.37 %. The ensemble diversity is 7.38. The centroid secondary structure in dot-bracket notation with a minimum free energy of -6.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Neisseria meningitidis, PreQ1 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Neisseria meningitidis, PreQ1 type switch.

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

SE4432667

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

Sequence

TCATGTCTAGTTTTTTATAGAGGGTTTCGGCTAGGAACCTCTGTTAT

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis , PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 9 nt. 2) Cytosine(C) in the sequence= 7 nt. 3) Guanine(G) in the sequence= 11 nt. 4) Thiamine(T) in the sequence= 20 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 47 nt. 8) CG percentage of the sequence= 38.30% 9) *Melting temperature of the DNA based on the Wallace formula= 66.30oC 10) The entered DNA sequence(5-3) is-47 nt.: TCATGTCTAGTTTTTTATAGAGGGTTTCGGCTAGGAACCTCTGTTAT 11) The complementary(Com) sequence(3-5) is-47 nt.: AGTACAGATCAAAAAATATCTCCCAAAGCCGATCCTTGGAGACAATA 12) The reverse(Rev) sequence(3-5) is-47 nt.: TATTGTCTCCAAGGATCGGCTTTGGGAGATATTTTTTGATCTGTACT 13) The RevCom sequence(5-3) is-47 nt.: ATAACAGAGGTTCCTAGCCGAAACCCTCTATAAAAAACTAGACATGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-34 nt.: TCATGTCTAGTTTTTTATAGAGGGTTTCGGCTAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-34 nt.: ATAACAGAGGTTCCTAGCCGAAACCCTCTATAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis , PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis , PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -11.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -11.96 kcal/mol. The frequency of the MFE structure in the ensemble is 21.21 %. The ensemble diversity is 4.19. The centroid secondary structure in dot-bracket notation with a minimum free energy of -11.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis , PreQ1 type switch.

2D_Structure (A) (B)

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

SSa4332457

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Staphylococcus saprophyticus

Length of Switch in nucleotides

Sequence

TATAAAGAGGTTCCTAGCTGATACCCTCTATAAAAAACTAGACACAT

Above is displayed the nucleotide sequence of the Staphylococcus saprophyticus , PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 19 nt. 2) Cytosine(C) in the sequence= 10 nt. 3) Guanine(G) in the sequence= 6 nt. 4) Thiamine(T) in the sequence= 12 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 47 nt. 8) CG percentage of the sequence= 34.04% 9) *Melting temperature of the DNA based on the Wallace formula= 64.55oC 10) The entered DNA sequence(5-3) is-47 nt.: TATAAAGAGGTTCCTAGCTGATACCCTCTATAAAAAACTAGACACAT 11) The complementary(Com) sequence(3-5) is-47 nt.: ATATTTCTCCAAGGATCGACTATGGGAGATATTTTTTGATCTGTGTA 12) The reverse(Rev) sequence(3-5) is-47 nt.: TACACAGATCAAAAAATATCTCCCATAGTCGATCCTTGGAGAAATAT 13) The RevCom sequence(5-3) is-47 nt.: ATGTGTCTAGTTTTTTATAGAGGGTATCAGCTAGGAACCTCTTTATA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-34 nt.: TATAAAGAGGTTCCTAGCTGATACCCTCTATAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-34 nt.: ATGTGTCTAGTTTTTTATAGAGGGTATCAGCTAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus saprophyticus , PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus saprophyticus , PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -5.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -5.91 kcal/mol. The frequency of the MFE structure in the ensemble is 31.46 %. The ensemble diversity is 5.57. The centroid secondary structure in dot-bracket notation with a minimum free energy of -5.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus saprophyticus , PreQ1 type switch.

2D_Structure (A) (B)

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

SA676557

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RiboSwitch type

PreQ1 type switch

Bacteria strain target

Streptococcus agalactiae

Length of Switch in nucleotides

Sequence

AGTCACTTAGTTTTTTATTCTGGGAAGTTTTCGAACCAGTCCGAG

Above is displayed the nucleotide sequence of the Streptococcus agalactiae , PreQ1 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 10 nt. 2) Cytosine(C) in the sequence= 8 nt. 3) Guanine(G) in the sequence= 10 nt. 4) Thiamine(T) in the sequence= 17 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 45 nt. 8) CG percentage of the sequence= 40.00% 9) *Melting temperature of the DNA based on the Wallace formula= 66.36oC 10) The entered DNA sequence(5-3) is-45 nt.: AGTCACTTAGTTTTTTATTCTGGGAAGTTTTCGAACCAGTCCGAG 11) The complementary(Com) sequence(3-5) is-45 nt.: TCAGTGAATCAAAAAATAAGACCCTTCAAAAGCTTGGTCAGGCTC 12) The reverse(Rev) sequence(3-5) is-45 nt.: GAGCCTGACCAAGCTTTTGAAGGGTCTTATTTTTTGATTCACTGA 13) The RevCom sequence(5-3) is-45 nt.: CTCGGACTGGTTCGAAAACTTCCCAGAATAAAAAACTAAGTGACT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-33 nt.: AGTCACTTAGTTTTTTATTCTGGGAAGTTTTCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-33 nt.: CTCGGACTGGTTCGAAAACTTCCCAGAATAAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus agalactiae , PreQ1 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus agalactiae , PreQ1 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -4.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -4.96 kcal/mol. The frequency of the MFE structure in the ensemble is 20.95 %. The ensemble diversity is 9.28. The centroid secondary structure in dot-bracket notation with a minimum free energy of -0.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus agalactiae , PreQ1 type switch.

2D_Structure (A) (B)

Multiple alignment of the PreQ1 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the PreQ1 type switches involved in.

Multi_resistance strains for the PreQ1 type switches

RiboSwitch_ID:

AB112357

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Acinetobacter baumannii

Length of Switch in nucleotides

197

Sequence

AGCATAAATGCCTATGACCTACCCCTCCTGCTAGCCAAATATCATAAAATGATTGCAGAGTGGTAAATCAAAGGTCTTGCCAACTCAGGAACGATGAGACGTTTAAGCTATGATGACCATGTTCTGTTGAACAATTATGTTGACCATCACCTATTCACATTTGCTGTGAATAGCGGCTACTCCCCAATGAAGTATGG

Above is displayed the nucleotide sequence of the Acinetobacter baumannii , Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 61 nt. 2) Cytosine(C) in the sequence= 44 nt. 3) Guanine(G) in the sequence= 38 nt. 4) Thiamine(T) in the sequence= 54 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 197 nt. 8) CG percentage of the sequence= 41.62% 9) *Melting temperature of the DNA based on the Wallace formula= 78.55oC 10) The entered DNA sequence(5-3) is-197 nt.: AGCATAAATGCCTATGACCTACCCCTCCTGCTAGCCAAATATCATAAAATGATTGCAGAGTGGTAAATCAAAGGTCTTGCCAACTCAGGAACGATGAGACGTTTAAGCTATGATGACCATGTTCTGTTGAACAATTATGTTGACCATCACCTATTCACATTTGCTGTGAATAGCGGCTACTCCCCAATGAAGTATGG 11) The complementary(Com) sequence(3-5) is-197 nt.: TCGTATTTACGGATACTGGATGGGGAGGACGATCGGTTTATAGTATTTTACTAACGTCTCACCATTTAGTTTCCAGAACGGTTGAGTCCTTGCTACTCTGCAAATTCGATACTACTGGTACAAGACAACTTGTTAATACAACTGGTAGTGGATAAGTGTAAACGACACTTATCGCCGATGAGGGGTTACTTCATACC 12) The reverse(Rev) sequence(3-5) is-197 nt.: GGTATGAAGTAACCCCTCATCGGCGATAAGTGTCGTTTACACTTATCCACTACCAGTTGTATTAACAAGTTGTCTTGTACCAGTAGTATCGAATTTGCAGAGTAGCAAGGACTCAACCGTTCTGGAAACTAAATGGTGAGACGTTAGTAAAATACTATAAACCGATCGTCCTCCCCATCCAGTATCCGTAAATACGA 13) The RevCom sequence(5-3) is-197 nt.: CCATACTTCATTGGGGAGTAGCCGCTATTCACAGCAAATGTGAATAGGTGATGGTCAACATAATTGTTCAACAGAACATGGTCATCATAGCTTAAACGTCTCATCGTTCCTGAGTTGGCAAGACCTTTGATTTACCACTCTGCAATCATTTTATGATATTTGGCTAGCAGGAGGGGTAGGTCATAGGCATTTATGCT 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-109 nt.: AGCATAAATGCCTATGACCTACCCCTCCTGCTAGCCAAATATCATAAAATGATTGCAGAGTGGTAAATCAAAGGTCTTGCCAACTCAGGAACGATGAGACGTTTAAGCT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-109 nt.: CCATACTTCATTGGGGAGTAGCCGCTATTCACAGCAAATGTGAATAGGTGATGGTCAACATAATTGTTCAACAGAACATGGTCATCATAGCTTAAACGTCTCATCGTTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Acinetobacter baumannii , Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Acinetobacter baumannii , Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -27.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -29.72 kcal/mol. The frequency of the MFE structure in the ensemble is 1.42 %. The ensemble diversity is 33.53. The centroid secondary structure in dot-bracket notation with a minimum free energy of -18.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Acinetobacter baumannii , Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Acinetobacter baumannii , Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Below is presented the sequences alignment of all the Mn+2 type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Mn+2 type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Mn+2 riboswitches and shorter motifs based on the general one: 1) N{0,28}YN{0,14}RRRN?YYRCRTCATGRN?YN{0,4}RN?YCATGGYGYRRN?YRGYN{0,88} 2) YCATGGYGYRR 3) YYRCRTCATGR Motifs identified amongst the Mn+2 riboswitches based on the sequences alignment: 1) MBDNYND 2) ATGTTGA 3) ATTACGAAGA 4) NKNWDYHBYHMR 5) GGNTACTNCCC Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

The table displays known human pathogenic bacteria bearing the Mn+2 type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BP198707

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Bordetella pertussis

Length of Switch in nucleotides

194

Sequence

GGCTCGCCCGGCAGGGTGAACGCATCGCGGCCAAAGGTCTCGCCGGGCTGCTGCGCGCGGATGATCCGTGCGTGCGGGCCGTCAGCGCCATGGGGTACGAAACCACCAAGTGTGTTGACG CTGACTCTCTGGAGCCGGCCTCTGTTCGGAGACGGATCCGGGGATAGAGATGGTTACTCCCCAATGACAGTGCG

Above is displayed the nucleotide sequence of the Bordetella pertussis , Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 57 nt. 3) Guanine(G) in the sequence= 70 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 194 nt. 8) CG percentage of the sequence= 65.46% 9) *Melting temperature of the DNA based on the Wallace formula= 88.27oC 10) The entered DNA sequence(5-3) is-194 nt.: GGCTCGCCCGGCAGGG-TGAACGCATCGCGGCCAAAGGTCTCGCCGGGCTGCTGCGCGCGGAT-GATCCGTGCGTGCGGGCCGTCAGCGCCATGGGGTACGAAACCACCAAGTGTGTTGACGCT-GACTCTCTGGAGCCGGCCTCTGTTCGGAGACGGATCCGGGGATAGAGATGGTTACTCCCCAAT-GACAGTGCG 11) The complementary(Com) sequence(3-5) is-194 nt.: CCGAGCGGGCCGTCCCACTTGCGTAGCGCCGGTTTCCAGAGCGGCCCGACGACGCGCGCCTACTAGGCACGCACGCCCGGCAGTCGCGGTACCCCATGCTTTGGTGGTTCACACAACTGCGACTGAGAGACCTCGGCCGGAGACAAGCCTCTGCCTAGGCCCCTATCTCTACCAATGAGGGGTTACTGTCACGC 12) The reverse(Rev) sequence(3-5) is-194 nt.: GCGT-GACAGTAACCCCTCATTGGTAGAGATAGGGGCCTAGGCAGAGGCTT-GTCTCCGGCCGAGGTCTCTCAGTCGCAGTTGTGTGAACCACCAAAGCATGGGG-TACCGCGACTGCCGGGCGTGCGTGCC-TAG-TAGGCGCGCGTCGTCGGGCCGCTCTGGAAACCGGCGCTACGCAAGTGGGACGGCCCGCTCGG 13) The RevCom sequence(5-3) is-194 nt.: CGCACTGTCATTGGGGAGTAACCATCTCTATCCCCGGATCCGTCTCCGAACAGAGGCCGGCTCCAGAGAGTCAGCGTCAACACACTTGGTGGTTTCGTACCCCATGGCGCTGACGGCCCGCACGCACGGATCATCCGCGCGCAGCAGCCCGGCGAGACCTTTGGCCGCGATGCGTTCACCCTGCCGGGCGAGCC 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-107 nt.: GGCTCGCCCGGCAGGG-TGAACGCATCGCGGCCAAAGGTCTCGCCGGGCTGCTGCGCGCGGAT-GATCCGTGCGTGCGGGCCGTCAGCGCCATGGGGTACGAAACCACC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-107 nt.: CGCACTGTCATTGGGGAGTAACCATCTCTATCCCCGGATCCGTCTCCGAACAGAGGCCGGCTCCAGAGAGTCAGCGTCAACACACTTGGTGGTTTCGTACCCCATGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bordetella pertussis , Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bordetella pertussis , Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -85.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -89.41 kcal/mol. The frequency of the MFE structure in the ensemble is 0.24 %. The ensemble diversity is 67.82. The centroid secondary structure in dot-bracket notation with a minimum free energy of -61.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bordetella pertussis , Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bordetella pertussis , Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

ENsp13404

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Enterobacter sp

Length of Switch in nucleotides

191

Sequence

AGTCCTGACCGGGGATAATCCATATGACACATCACTGCCCCCAGTAAACAGCAGTTGATGTATCAATGGTCTCGCCTGAGCACCTTCGGCAATGCAGAAGATGATCCGTATACGCCACGTTTTTTTAAACGAGTATGTTGACGTATACATTTCCCGGGTAAGGAAATCGGCTACTCCCCAACGACGGGCGC

Above is displayed the nucleotide sequence of the Enterobacter sp, Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 51 nt. 2) Cytosine(C) in the sequence= 51 nt. 3) Guanine(G) in the sequence= 44 nt. 4) Thiamine(T) in the sequence= 45 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 191 nt. 8) CG percentage of the sequence= 49.74% 9) *Melting temperature of the DNA based on the Wallace formula= 81.77oC 10) The entered DNA sequence(5-3) is-191 nt.: AGTCCTGACCGGGGATAATCCATATGACACATCACTGCCCCCAGTAAACAGCAGTTGATGTATCAATGGTCTCGCCTGAGCACCTTCGGCAATGCAGAAGATGATCCGTATACGCCACGTTTTTTTAAACGAGTATGTTGACGTATACATTTCCCGGGTAAGGAAATCGGCTACTCCCCAACGACGGGCGC 11) The complementary(Com) sequence(3-5) is-191 nt.: TCAGGACTGGCCCCTATTAGGTATACTGTGTAGTGACGGGGGTCATTTGTCGTCAACTACATAGTTACCAGAGCGGACTCGTGGAAGCCGTTACGTCTTCTACTAGGCATATGCGGTGCAAAAAAATTTGCTCATACAACTGCATATGTAAAGGGCCCATTCCTTTAGCCGATGAGGGGTTGCTGCCCGCG 12) The reverse(Rev) sequence(3-5) is-191 nt.: CGCGGGCAGCAACCCCTCATCGGCTAAAGGAATGGGCCCTTTACATATGCAGTTGTATGAGCAAATTTTTTTGCACCGCATATGCCTAGTAGAAGACGTAACGGCTTCCACGAGTCCGCTCTGGTAACTATGTAGTTGACGACAAATGACCCCCGTCACTACACAGTATACCTAATAGGGGCCAGTCCTGA 13) The RevCom sequence(5-3) is-191 nt.: GCGCCCGTCGTTGGGGAGTAGCCGATTTCCTTACCCGGGAAATGTATACGTCAACATACTCGTTTAAAAAAACGTGGCGTATACGGATCATCTTCTGCATTGCCGAAGGTGCTCAGGCGAGACCATTGATACATCAACTGCTGTTTACTGGGGGCAGTGATGTGTCATATGGATTATCCCCGGTCAGGACT 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-106 nt.: AGTCCTGACCGGGGATAATCCATATGACACATCACTGCCCCCAGTAAACAGCAGTTGATGTATCAATGGTCTCGCCTGAGCACCTTCGGCAATGCAGAAGATGATC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-106 nt.: GCGCCCGTCGTTGGGGAGTAGCCGATTTCCTTACCCGGGAAATGTATACGTCAACATACTCGTTTAAAAAAACGTGGCGTATACGGATCATCTTCTGCATTGCCGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterobacter sp, Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterobacter sp, Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -54.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -57.47 kcal/mol. The frequency of the MFE structure in the ensemble is 0.69 %. The ensemble diversity is 28.62. The centroid secondary structure in dot-bracket notation with a minimum free energy of -47.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterobacter sp, Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterobacter sp, Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

LM113657

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

104

Sequence

ACAAATGTCAGAGGGGAGTAGCGCTGATTAGCTTTTTAATCAGGATAAAGTCGTCATTACATGATAGAGATATCATCGGTTTTATCACATTTAACTTTAAATGT

Above is displayed the nucleotide sequence of the Listeria monocytogenes, Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 14 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 35 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 104 nt. 8) CG percentage of the sequence= 33.65% 9) *Melting temperature of the DNA based on the Wallace formula= 72.23oC 10) The entered DNA sequence(5-3) is-104 nt.: ACAAATGTCAGAGGGGAGTAGCGCTGATTAGCTTTTTAATCAGGATAAAGTCGTCATTACATGATAGAGATATCATCGGTTTTATCACATTTAACTTTAAATGT 11) The complementary(Com) sequence(3-5) is-104 nt.: TGTTTACAG-TCTCCCCTCATCGCGACTAATCGAAAAATTAGTCCTATTTCAGCAGTAATGTACTATCTC-TATAGTAGCCAAAATAGTGTAAATTGAAATTTACA 12) The reverse(Rev) sequence(3-5) is-104 nt.: TGTAAATTTCAATTTACACTATTTTGGCTACTATAGAGATAGTACATTACTGCTGAAATAGGACTAATTTTTCGATTAGTCGCGATGAGGGGAGACTGTAAACA 13) The RevCom sequence(5-3) is-104 nt.: ACATTTAAAGTTAAATGTGA-TAAAACCGATGATATCTCTATCATGTAATGACGACTTTATCCTGATTAAAAA-GCTAATCAGCGCTACTCCCCTCTGACATTTGT 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-62 nt.: ACAAATGTCAGAGGGGAGTAGCGCTGATTAGCTTTTTAATCAGGATAAAGTCGTCATTACAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-62 nt.: ACATTTAAAGTTAAATGTGATAAAACCGATGATATCTCTATCATGTAATGACGACTTTATCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes, Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes, Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -19.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -20.70 kcal/mol. The frequency of the MFE structure in the ensemble is 12.15%. The ensemble diversity is 16.58. The centroid secondary structure in dot-bracket notation with a minimum free energy of -19.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes, Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes, Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

PA675557

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Pseudomonas aeruginosa

Length of Switch in nucleotides

166

Sequence

CCAGCCGGGCATGAGTCAACGACATGACCCCGCGGCCCGGCTTCGGCGCAGGAATGTCGTTGGTCTCACCAATCCGGTTGGATGCGCTGGCCATGGCAGGTTGCCAAGAATGTTGACCAGCGCGCCGTCAACGGGTGACGGCAGGCTACTCCCCAAGGAAGGCCGG

Above is displayed the nucleotide sequence of the Pseudomonas aeruginosa, Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 52 nt. 3) Guanine(G) in the sequence= 56 nt. 4) Thiamine(T) in the sequence= 26 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 166 nt. 8) CG percentage of the sequence= 65.06% 9) *Melting temperature of the DNA based on the Wallace formula= 87.52oC 10) The entered DNA sequence(5-3) is-166 nt.: CCAGCCGGGCATGAGTCAACGACATGACCCCGCGGCCCGGCTTCGGCGCAGGAATGTCGTTGGTCTCACCAATCCGGTTGGATGCGCTGGCCATGGCAGGTTGCCAAGAATGTTGACCAGCGCGCCGTCAACGGGTGACGGCAGGCTACTCCCCAAGGAAGGCCGG 11) The complementary(Com) sequence(3-5) is-166 nt.: GGTCGGCCCGTACTCAGTTGCTGTACTGGGGCGCCGGGCCGAAGCCGCGTCCTTACAGCAACCAGAGTGGTTAGGCCAACCTACGCGACCGGTACCGTCCAACGGTTCTTACAACTGGTCGCGCGGCAGTTGCCCACTGCCGTCCGATGAGGGGTTCCTTCCGGCC 12) The reverse(Rev) sequence(3-5) is-166 nt.: GGCCGGAAGGAACCCCTCATCGGACGGCAGTGGGCAACTGCCGCGCGACCAGTTGTAAGAACCGTTGGACGGTACCGGTCGCGTAGGTTGGCCTAACCACTCTGGTTGCTGTAAGGACGCGGCTTCGGCCCGGCGCCCCAGTACAGCAACTGAGTACGGGCCGACC 13) The RevCom sequence(5-3) is-166 nt.: CCGGCCTTCCTTGGGGAGTAGCCTGCCGTCACCCGTTGACGGCGCGCTGGTCAACATTCTTGGCAACCTGCCATGGCCAGCGCATCCAACCGGATTGGTGAGACCAACGACATTCCTGCGCCGAAGCCGGGCCGCGGGGTCATGTCGTTGACTCATGCCCGGCTGG 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-93 nt.: CCAGCCGGGCATGAGTCAACGACATGACCCCGCGGCCCGGCTTCGGCGCAGGAATGTCGTTGGTCTCACCAATCCGGTTGGATGCGCTGGCCA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-93 nt.: CCGGCCTTCCTTGGGGAGTAGCCTGCCGTCACCCGTTGACGGCGCGCTGGTCAACATTCTTGGCAACCTGCCATGGCCAGCGCATCCAACCGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Pseudomonas aeruginosa, Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Pseudomonas aeruginosa, Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -80.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -82.21 kcal/mol. The frequency of the MFE structure in the ensemble is 10.19%. The ensemble diversity is 7.60. The centroid secondary structure in dot-bracket notation with a minimum free energy of -80.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Pseudomonas aeruginosa, Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Pseudomonas aeruginosa, Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

SE215258

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Salmonella enterica

Length of Switch in nucleotides

102

Sequence

GACCAGCGGCGGCTGGTCCGTACGCGCCACGTTTTGCAACGAGTATGTTGACGCGTACATTTCCGGAATCTGGAAATCGGCTACTCCCCAATTGACGGCGCA

Above is displayed the nucleotide sequence of the Salmonella enterica, Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 21 nt. 2) Cytosine(C) in the sequence= 30 nt. 3) Guanine(G) in the sequence= 29 nt. 4) Thiamine(T) in the sequence= 22 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 102 nt. 8) CG percentage of the sequence= 57.84% 9) *Melting temperature of the DNA based on the Wallace formula= 82.02oC 10) The entered DNA sequence(5-3) is-102 nt.: GACCAGCGGCGGCTGG-TCCGTACGCGCCACGTTTTGCAACGAGTATGTTGACGCGTACAT-TTCCGGAATCTGGAAATCGGCTACTCCCCAATTGACGGCGCA 11) The complementary(Com) sequence(3-5) is-102 nt.: CTGGTCGCCGCCGACCAGGCATGCGCGGTGCAAAACGTTGCTCATACAACTGCGCATGTAAAGGCCTTAGACCTTTAGCCGATGAGGGGTTAACTGCCGCGT 12) The reverse(Rev) sequence(3-5) is-102 nt.: ACGCGGCAGTTAACCCCTCATCGGCTAAAGGTCTAAGGCCTTTACATGCGCAGTTGTATGAGCAACGTTTTGCACCGCGCATGCCTGGTCGGCGGCGACCAG 13) The RevCom sequence(5-3) is-102 nt.: TGCGCCGTCAATTGGGGAG-TAGCCGATTTCCAGATTCCGGAAATGTACGCGTCAACATACTCGTTGCAAAACGTGGCGCG-TACGGACCAGCCGCCGCTGGTC 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-61 nt.: GACCAGCGGCGGCTGGTCCGTACGCGCCACGTTTTGCAACGAGTATGTT-GACGCGTACATT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-61 nt.: TGCGCCGTCAATTGGGGAGTAGCCGATTTCCA-GATTCCGGAAATGTACGCGTCAACATACT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella enterica, Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella enterica, Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -37.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.70 kcal/mol. The frequency of the MFE structure in the ensemble is 23.26%. The ensemble diversity is 10.79. The centroid secondary structure in dot-bracket notation with a minimum free energy of -37.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella enterica, Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella enterica, Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

SA559251

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Staphylococcus aureus

Length of Switch in nucleotides

107

Sequence

CATTTTGTCAGAGGGGAGTAACTTAAGAATCATGACCGTATAAATGATTCGACACTTTATCGTCATTACGAAGATATCTTCCGGTAAAGTGGGCAATTTAAATTGCT

Above is displayed the nucleotide sequence of the Staphylococcus aureus , Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 34 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 22 nt. 4) Thiamine(T) in the sequence= 34 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 107 nt. 8) CG percentage of the sequence= 36.45% 9) *Melting temperature of the DNA based on the Wallace formula= 73.56oC 10) The entered DNA sequence(5-3) is-107 nt.: CATTTTGTCAGAGGGGAGTAACTTAAGAATCATGACCGTATAAATGATTCGACACTTTATCGTCATTACGAAGATATCTTCCGGTAAAGTGGGCAATTTAAATTGCT 11) The complementary(Com) sequence(3-5) is-107 nt.: GTAAAACAGTCTCCCCTCATTGAATTCTTAGTACTGGCATATTTACTAAGCTGTGAAATAGCAGTAATGCTTCTATAGAAGGCCATTTCACCCGTTAAATTTAACGA 12) The reverse(Rev) sequence(3-5) is-107 nt.: TCGTTAAATTTAACGGGTGAAATGGCCTTCTATAGAAGCATTACTGCTATTTCACAGCTTAGTAAATATGCCAGTACTAAGAATTCAATGAGGGGAGACTGTTTTAC 13) The RevCom sequence(5-3) is-107 nt.: AGCAATTTAAATTGCCCACTTTACCGGAAGATATCTTCGTAATGACGATAAAGTGTCGAATCATTTATACGGTCATGATTCTTAAGTTACTCCCCTCTGACAAAATG 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-64 nt.: CATTTTGTCAGAGGGGAGTAACTTAAGAATCATGACCGTATAAATGATTCGACACTTTATCGTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-64 nt.: AGCAATTTAAATTGCCCACTTTACCGGAAGATATCTTCGTAATGACGATAAAGTGTCGAATCAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus , Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus , Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -24.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -25.50 kcal/mol. The frequency of the MFE structure in the ensemble is 19.85%. The ensemble diversity is 9.29. The centroid secondary structure in dot-bracket notation with a minimum free energy of -23.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus , Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus , Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

SE665499

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

107

Sequence

AAAACTGTCAGAGGGGAGTAACTTGAGAATAGTTATTGAATGCATTTAAACCGATAATAACTATTCAACACTTTGTCGTCATTACGAAGATAAGTCTTCCGGTAAAGTGGGCAAAAATATTGCT

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis , Mn+2 type switch.

Sequence information and analysis

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis , Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis , Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -26.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -27.68 kcal/mol. The frequency of the MFE structure in the ensemble is 12.50%. The ensemble diversity is 7.83. The centroid secondary structure in dot-bracket notation with a minimum free energy of -26.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis , Mn+2 type switch.

2D_Structure (A) (B)

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

VC010686

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Vibrio cholerae

Length of Switch in nucleotides

110

Sequence

CGCTCCGTCTTTGGGGAGTAGCTGGTCTCTAAGTTTTCAACTTGGTGATTCACACATCAACATATTTGGTACTCAATTACCATGGTGTGTGAGACCTGAGCCTTCAGGTT

Above is displayed the nucleotide sequence of the Vibrio cholerae , Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 23 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 26 nt. 4) Thiamine(T) in the sequence= 37 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 110 nt. 8) CG percentage of the sequence= 45.45% 9) *Melting temperature of the DNA based on the Wallace formula= 77.42oC 10) The entered DNA sequence(5-3) is-110 nt.: CGCTCCGTCTTTGGGGAGTAGCTGGTCTCTAAGTTTTCAACTTGGTGATTCACACATCAACATATTTGGTACTCAATTACCATGGTGTGTGAGACCTGAGCCTTCAGGTT 11) The complementary(Com) sequence(3-5) is-110 nt.: GCGAGGCAGAAACCCCTCATCGACCAGAGATTCAAAAGTTGAACCACTAAGTGTGTAGTT-GTATAAACCATGAGTTAATGGTACCACACACTCTGGACTCGGAAGTCCAA 12) The reverse(Rev) sequence(3-5) is-110 nt.: TTGGACTTCCGAGTCCAGAGTGTGTGGTACCATTAACTCATGGTTTATACAACTACACACTTAGTGGTTCAACTTTTGAATCTCTGGTCGATGAGGGGTTTCTGCCTCGC 13) The RevCom sequence(5-3) is-110 nt.: AACCTGAAGGCTCAGGTCTCACACACCATGGTAATTGAGTACCAAATATGTTGATGTGTGAATCACCAAGTTGAAAACTTAGAGACCAGCTACTCCCCAAAGACGGAGCG 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-65 nt.: CGCTCCGTCTTTGGGGAGTAGCTGGTCTCTAAGTTTTCAACTTGGTGATTCACACATCAACATAT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: AACCTGAAGGCTCAGGTCTCACACACCATGGTAATTGAGTACCAAATATGTTGATGTGTGAATCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Vibrio cholerae , Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Vibrio cholerae , Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -39.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -40.59 kcal/mol. The frequency of the MFE structure in the ensemble is 23.48%. The ensemble diversity is 3.76. The centroid secondary structure in dot-bracket notation with a minimum free energy of -39.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Vibrio cholerae , Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Vibrio cholerae , Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

YP030623

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RiboSwitch type

Mn+2 type switch

Bacteria strain target

Yersinia pestis

Length of Switch in nucleotides

200

Sequence

TCGGCCGGGCGGCTCCATATACACGTAACCCACCCCCAACCTAACGACGGAGCTACGTGTCTATGGTCTCGCCAACCTTACCTGGCTGCCCGTACCACGTTTCAAATAAATGAAACGAGTATGTTGATACGGGCGTTTCTGCTTGCCAATATATTATGAATATATTGCACAGAAACCGGCTACTCCCCATGAACGGCGCA

Above is displayed the nucleotide sequence of the Yersinia pestis, Mn+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 52 nt. 2) Cytosine(C) in the sequence= 60 nt. 3) Guanine(G) in the sequence= 42 nt. 4) Thiamine(T) in the sequence= 46 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 200 nt. 8) CG percentage of the sequence= 51.00% 9) *Melting temperature of the DNA based on the Wallace formula= 82.45oC 10) The entered DNA sequence(5-3) is-200 nt.: TCGGCCGGGCGGCTCCATATACACGTAACCCACCCCCAACCTAACGACGGAGCTACGTGTCTATGGTCTCGCCAACCTTACCTGGCTGCCCGTACCACGTTTCAAATAAATGAAACGAGTATGTTGATACGGGCGTTTCTGCTTGCCAATATATTATGAATATATTGCACAGAAACCGGCTACTCCCCATGAACGGCGCA 11) The complementary(Com) sequence(3-5) is-200 nt.: AGCCGGCCCGCCGAGGTATATGTGCATTGGGTGGGGGTTGGATTGCTGCCTCGATGCACAGATACCAGAGCGGTTGGAATGGACCGACGGGCATGGTGCAAAGTTTATTTACTTTGCTCATACAACTATGCCCGCAAAGACGAACGGTTATATAATACTTATATAACGTGTCTTTGGCCGATGAGGGGTACTTGCCGCGT 12) The reverse(Rev) sequence(3-5) is-200 nt.: ACGCGGCAAGTACCCCTCATCGGCCAAAGACACGTTATATAAGTATTATATAACCGTTCGTCTTTGCGGGCATAGTTGTATGAGCAAAGTAAATAAACTTTGCACCATGCCCGTCGGTCCATTCCAACCGCTCTGGTATCTGTGCATCGAGGCAGCAATCCAACCCCCACCCAATGCACATATACCTCGGCGGGCCGGCT 13) The RevCom sequence(5-3) is-200 nt.: TGCGCCGTTCATGGGGAGTAGCCGGTTTCTGTGCAATATATTCATAATATATTGGCAAGCAGAAACGCCCGTATCAACATACTCGTTTCATTTATTTGAAACGTGGTACGGGCAGCCAGGTAAGGTTGGCGAGACCATAGACACGTAGCTCCGTCGTTAGGTTGGGGGTGGGTTACGTGTATATGGAGCCGCCCGGCCGA 14) The DNA sequence(5-3) to order with a 10nt overlapping re-gion-110 nt.: TCGGCCGGGCGGCTCCATATACACGTAACCCACCCCCAACCTAACGACGGAGCTACGTGTCTATGGTCTCGCCAACCTTACCTGGCTGCCCGTACCACGTTTCAAATAAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-110 nt.: TGCGCCGTTCATGGGGAGTAGCCGGTTTCTGTGCAATATATTCATAATATATTGGCAAGCAGAAACGCCCGTATCAACATACTCGTTTCATTTATTTGAAACGTGGTACG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Yersinia pestis, Mn+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Yersinia pestis, Mn+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -65.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -68.49 kcal/mol. The frequency of the MFE structure in the ensemble is 1.08%. The ensemble diversity is 14.22. The centroid secondary structure in dot-bracket notation with a minimum free energy of -62.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Yersinia pestis, Mn+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Yersinia pestis, Mn+2 type switch.

Multiple alignment of the Mn+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mn+2 type switches involved in.

Multi_resistance strains for the Mn+2 type switches

RiboSwitch_ID:

EC035467

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RiboSwitch type

Mg+2 type switch

Bacteria strain target

Escherichia coli

Length of Switch in nucleotides

116

Sequence

CTTACCGGAGGTTATATGGAACCTGATCCCACGCCTCTCCCTCGACGGAGATTAAAACTTTTCCGGTAAGCCCGTCTTTTCACGGCGTTACCGGATGCGTAAGGCCGTGACGTTTT

Above is displayed the nucleotide sequence of the Escherichia coli, Mg+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 23 nt. 2) Cytosine(C) in the sequence= 33 nt. 3) Guanine(G) in the sequence= 28 nt. 4) Thiamine(T) in the sequence= 32 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 116 nt. 8) CG percentage of the sequence= 52.59% 9) *Melting temperature of the DNA based on the Wallace formula= 80.66oC 10) The entered DNA sequence(5-3) is-116 nt.: CTTACCGGAGGTTATATGGAACCTGATCCCACGCCTCTCCCTCGACGGAGATTAAAACTTTTCCGGTAAGCCCGTCTTTTCACGGCGTTACCGGATGCGTAAGGCCGTGACGTTTT 11) The complementary(Com) sequence(3-5) is-116 nt.: GAATGGCCTCCAATATACCTTGGACTAGGGTGCGGAGAGGGAGCTGCCTCTAATTTTGAAAAGGCCATTCGGGCAGAAAAGTGCCGCAATGGCCTACGCATTCCGGCACTGCAAAA 12) The reverse(Rev) sequence(3-5) is-116 nt.: TTTTGCAGTGCCGGAATGCGTAGGCCATTGCGGCACTTTTCTGCCCGAATGGCCTTTTCAAAATTAGAGGCAGCTCCCTCTCCGCACCCTAGTCCAAGGTATATTGGAGGCCATTC 13) The RevCom sequence(5-3) is-116 nt.: AAAACGTCACGGCCTTACGCATCCGGTAACGCCGTGAAAAGACGGGCTTACCGGAAAAGTTTTAATCTCCGTCGAGGGAGAGGCGTGGGATCAGGTTCCATATAACCTCCGGTAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-68 nt.: CTTACCGGAGGTTATATGGAACCTGATCCCACGCCTCTCCCTCGACGGAGATTAAAACTTTTCCGGTA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-68 nt.: AAAACGTCACGGCCTTACGCATCCGGTAACGCCGTGAAAAGACGGGCTTACCGGAAAAGTTTTAATCT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Escherichia coli, Mg+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Escherichia coli, Mg+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -38.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -40.76 kcal/mol. The frequency of the MFE structure in the ensemble is 3.01 %. The ensemble diversity is 12.66. The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Escherichia coli, Mg+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Escherichia coli, Mg+2 type switch.

Multiple alignment of the Mg+2 type switches

Below is presented the sequences alignment of all the Mg+2 type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Mg+2 type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Mg+2 riboswitches and shorter motifs based on the general one: 1) CTTACCGGAGRN{0,3}TATGGAN?CCYGATCCCACN?CCTCN?YCCN?CGAYGGAGN{0,7}YYTTTCCGGTAAGCCYGYYTN{0,3}RCN?GYN?TTACCGGN{0,2}GYGTAARGCN?GTGACGTYN?T 2) YYTTTCCGGTAAGCCYGYYT 3) CTTACCGGAGR Motifs identified amongst the Mg+2 riboswitches based on the sequences alignment: 1) RCCCTCTNCC 2) RCNCCTCW 3) TTTCCGGTAAGCCNG 4) CRSKGYBY Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Mg+2 type switches involved in.

Multi_resistance strains for the Mg+2 type switches

The table displays known human pathogenic bacteria bearing the Mg+2 type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

SD551067

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RiboSwitch type

Mg+2 type switch

Bacteria strain target

Shigella dysenteriae

Length of Switch in nucleotides

116

Sequence

CTTACCGGAGGTTATATGGAACCTGATCCCACGCCTCTCCCTCGACGGAGATTAAAACTTTTCCGGTAAGCCCGTCTTTTCACGGCGTTACCGGATGCGTAAGGCCGTGACGTTTT

Above is displayed the nucleotide sequence of the Shigella dysenteriae , Mg+2 type switch.

Sequence information and analysis

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Shigella dysenteriae , Mg+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Shigella dysenteriae , Mg+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Shigella dysenteriae , Mg+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Shigella dysenteriae , Mg+2 type switch.

Multiple alignment of the Mg+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mg+2 type switches involved in.

Multi_resistance strains for the Mg+2 type switches

RiboSwitch_ID:

ST511767

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RiboSwitch type

Mg+2 type switch

Bacteria strain target

Salmonella Typhimurium

Length of Switch in nucleotides

113

Sequence

CTTACCGGAGGCGACATGGACCCTGAACCCACCCCTCTCCCGCGATGGAGAATTTTCCTTTTCCGGTAAGCCTGCCTCTGCTGTCTTACCGGTGTGTAAGACAGTGACACAAT

Above is displayed the nucleotide sequence of the Salmonella Typhimurium , Mg+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 23 nt. 2) Cytosine(C) in the sequence= 36 nt. 3) Guanine(G) in the sequence= 26 nt. 4) Thiamine(T) in the sequence= 28 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 113 nt. 8) CG percentage of the sequence= 54.87% 9) *Melting temperature of the DNA based on the Wallace formula= 81.45oC 10) The entered DNA sequence(5-3) is-113 nt.: CTTACCGGAGGCGACATGGACCCTGAACCCACCCCTCTCCCGCGATGGAGAATTTTCCTTTTCCGGTAAGCCTGCCTCTGCTGTCTTACCGGTGTGTAAGACAGTGACACAAT 11) The complementary(Com) sequence(3-5) is-113 nt.: GAATGGCCTCCGCTGTACCTGGGACTTGGGTGGGGAGAGGGCGCTACCTCTTAAAAGGAAAAGGCCATTCGGACGGAGACGACAGAATGGCCACACATTCTGTCACTGTGTTA 12) The reverse(Rev) sequence(3-5) is-113 nt.: TAACACAGTGACAGAATGTGTGGCCATTCTGTCGTCTCCGTCCGAATGGCCTTTTCCTTTTAAGAGGTAGCGCCCTCTCCCCACCCAAGTCCCAGGTACAGCGGAGGCCATTC 13) The RevCom sequence(5-3) is-113 nt.: ATTGTGTCACTGTCTTACACACCGGTAAGACAGCAGAGGCAGGCTTACCGGAAAAGGAAAATTCTCCATCGCGGGAGAGGGGTGGGTTCAGGGTCCATGTCGCCTCCGGTAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-67 nt.: CTTACCGGAGGCGACATGGACCCTGAACCCACCCCTCTCCCGCGATGGAGAATTTTCCTTTTCCGGT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-67 nt.: ATTGTGTCACTGTCTTACACACCGGTAAGACAGCAGAGGCAGGCTTACCGGAAAAGGAAAATTCTCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella Typhimurium , Mg+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella Typhimurium , Mg+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -33.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -35.89 kcal/mol. The frequency of the MFE structure in the ensemble is 3.39 %. The ensemble diversity is 12.89. The centroid secondary structure in dot-bracket notation with a minimum free energy of -31.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella Typhimurium , Mg+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella Typhimurium , Mg+2 type switch.

Multiple alignment of the Mg+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mg+2 type switches involved in.

Multi_resistance strains for the Mg+2 type switches

RiboSwitch_ID:

SE576797

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RiboSwitch type

Mg+2 type switch

Bacteria strain target

Salmonella enterica

Length of Switch in nucleotides

113

Sequence

ATTGTGTCACTGTCTTACACACCGGTAAGACAGCAGAGGCAGGCTTACCGGAAAAGGAAAATTCTCCATCGCGGGAGAGGGGTGGGTTCAGGGTCCATGTCGCCTCCGGTAAG

Above is displayed the nucleotide sequence of the Salmonella enterica, Mg+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 28 nt. 2) Cytosine(C) in the sequence= 26 nt. 3) Guanine(G) in the sequence= 36 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 113 nt. 8) CG percentage of the sequence= 54.87% 9) *Melting temperature of the DNA based on the Wallace formula= 81.45oC 10) The entered DNA sequence(5-3) is-113 nt.: ATTGTGTCACTGTCTTACACACCGGTAAGACAGCAGAGGCAGGCTTACCGGAAAAGGAAAATTCTCCATCGCGGGAGAGGGGTGGGTTCAGGGTCCATGTCGCCTCCGGTAAG 11) The complementary(Com) sequence(3-5) is-113 nt.: TAACACAGTGACAGAATGTGTGGCCATTCTGTCGTCTCCGTCCGAATGGCCTTTTCCTTTTAAGAGGTAGCGCCCTCTCCCCACCCAAGTCCCAGGTACAGCGGAGGCCATTC 12) The reverse(Rev) sequence(3-5) is-113 nt.: GAATGGCCTCCGCTGTACCTGGGACTTGGGTGGGGAGAGGGCGCTACCTCTTAAAAGGAAAAGGCCATTCGGACGGAGACGACAGAATGGCCACACATTCTGTCACTGTGTTA 13) The RevCom sequence(5-3) is-113 nt.: CTTACCGGAGGCGACATGGACCCTGAACCCACCCCTCTCCCGCGATGGAGAATTTTCCTTTTCCGGTAAGCCTGCCTCTGCTGTCTTACCGGTGTGTAAGACAGTGACACAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-67 nt.: ATTGTGTCACTGTCTTACACACCGGTAAGACAGCAGAGGCAGGCTTACCGGAAAAGGAAAATTCTCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-67 nt.: CTTACCGGAGGCGACATGGACCCTGAACCCACCCCTCTCCCGCGATGGAGAATTTTCCTTTTCCGGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Salmonella enterica, Mg+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Salmonella enterica, Mg+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -42.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -44.03 kcal/mol. The frequency of the MFE structure in the ensemble is 8.32 %. The ensemble diversity is 5.53. The centroid secondary structure in dot-bracket notation with a minimum free energy of -42.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Salmonella enterica, Mg+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Salmonella enterica, Mg+2 type switch.

Multiple alignment of the Mg+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mg+2 type switches involved in.

Multi_resistance strains for the Mg+2 type switches

RiboSwitch_ID:

EB553099

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RiboSwitch type

Mg+2 type switch

Bacteria strain target

Enterobacter

Length of Switch in nucleotides

111

Sequence

CTTACCGGAGGCTGTATGGACCCTGATCCCACCCCTCTCCCGCGATGGAGAATCTCTTTCCGGTAAGCCAGCCCTCGCTGTCTCACCGGTGATGTGAGGCAGCAACGTCAT

Above is displayed the nucleotide sequence of the Enterobacter , Mg+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 38 nt. 3) Guanine(G) in the sequence= 28 nt. 4) Thiamine(T) in the sequence= 25 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 111 nt. 8) CG percentage of the sequence= 59.46% 9) *Melting temperature of the DNA based on the Wallace formula= 83.22oC 10) The entered DNA sequence(5-3) is-111 nt.: CTTACCGGAGGCTGTATGGACCCTGATCCCACCCCTCTCCCGCGATGGAGAATCTCTTTCCGGTAAGCCAGCCCTCGCTGTCTCACCGGTGATGTGAGGCAGCAACGTCAT 11) The complementary(Com) sequence(3-5) is-111 nt.: GAATGGCCTCCGACATACCTGGGACTAGGGTGGGGAGAGGGCGCTACCTCTTAGAGAAAGGCCATTCGGTCGGGAGCGACAGAGTGGCCACTACACTCCGTCGTTGCAGTA 12) The reverse(Rev) sequence(3-5) is-111 nt.: TACTGCAACGACGGAGTGTAGTGGCCACTCTGTCGCTCCCGACCGAATGGCCTTTCTCTAAGAGGTAGCGCCCTCTCCCCACCCTAGTCCCAGGTATGTCGGAGGCCATTC 13) The RevCom sequence(5-3) is-111 nt.: ATGACGTTGCTGCCTCACATCACCGGTGAGACAGCGAGGGCTGGCTTACCGGAAAGAGATTCTCCATCGCGGGAGAGGGGTGGGATCAGGGTCCATACAGCCTCCGGTAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-66 nt.: CTTACCGGAGGCTGTATGGACCCTGATCCCACCCCTCTCCCGCGATGGAGAATCTCTTTCCGGTAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-66 nt.: ATGACGTTGCTGCCTCACATCACCGGTGAGACAGCGAGGGCTGGCTTACCGGAAAGAGATTCTCCA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterobacter , Mg+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterobacter , Mg+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -37.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.78 kcal/mol. The frequency of the MFE structure in the ensemble is 10.61 %. The ensemble diversity is 8.41. The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterobacter , Mg+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterobacter , Mg+2 type switch.

Multiple alignment of the Mg+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mg+2 type switches involved in.

Multi_resistance strains for the Mg+2 type switches

RiboSwitch_ID:

KP162231

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RiboSwitch type

Mg+2 type switch

Bacteria strain target

Klebsiella pneumoniae

Length of Switch in nucleotides

117

Sequence

CTTACCGGAGATAGTTATGGACCCCGATCCCACTCCTCATCCTCGATGGAGCAACCTTTCTTTCCGGTAAGCCTGTTTAACACTGCTTTACCGGAAAGCGTAAAGCAGTGACGTCCT

Above is displayed the nucleotide sequence of the Klebsiella pneumoniae, Mg+2 type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 27 nt. 2) Cytosine(C) in the sequence= 35 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 31 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 117 nt. 8) CG percentage of the sequence= 50.43% 9) *Melting temperature of the DNA based on the Wallace formula= 79.83oC 10) The entered DNA sequence(5-3) is-117 nt.: CTTACCGGAGATAGTTATGGACCCCGATCCCACTCCTCATCCTCGATGGAGCAACCTTTCTTTCCGGTAAGCCTGTTTAACACTGCTTTACCGGAAAGCGTAAAGCAGTGACGTCCT 11) The complementary(Com) sequence(3-5) is-117 nt.: GAATGGCCTCTATCAATACCTGGGGCTAGGGTGAGGAGTAGGAGCTACCTCGTTGGAAAGAAAGGCCATTCGGACAAATTGTGACGAAATGGCCTTTCGCATTTCGTCACTGCAGGA 12) The reverse(Rev) sequence(3-5) is-117 nt.: TCCTGCAGTGACGAAATGCGAAAGGCCATTTCGTCACAATTTGTCCGAATGGCCTTTCTTTCCAACGAGGTAGCTCCTACTCCTCACCCTAGCCCCAGGTATTGATAGAGGCCATTC 13) The RevCom sequence(5-3) is-117 nt.: AGGACGTCACTGCTTTACGCTTTCCGGTAAAGCAGTGTTAAACAGGCTTACCGGAAAGAAAGGTTGCTCCATCGAGGATGAGGAGTGGGATCGGGGTCCATAACTATCTCCGGTAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-69 nt.: CTTACCGGAGATAGTTATGGACCCCGATCCCACTCCTCATCCTCGATGGAGCAACCTTTCTTTCCGGTA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-69 nt.: AGGACGTCACTGCTTTACGCTTTCCGGTAAAGCAGTGTTAAACAGGCTTACCGGAAAGAAAGGTTGCTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Klebsiella pneumoniae, Mg+2 type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Klebsiella pneumoniae, Mg+2 type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -36.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -38.44 kcal/mol. The frequency of the MFE structure in the ensemble is 7.03 %. The ensemble diversity is 9.97. The centroid secondary structure in dot-bracket notation with a minimum free energy of -36.80 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Klebsiella pneumoniae, Mg+2 type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Klebsiella pneumoniae, Mg+2 type switch.

Multiple alignment of the Mg+2 type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Mg+2 type switches involved in.

Multi_resistance strains for the Mg+2 type switches

RiboSwitch_ID:

AB656576

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Acinetobacter baumannii

Length of Switch in nucleotides

Sequence

GGTAACGTAGGCATCATTAGCCAATACGGCGGTTTTTCAAGGGAGGAATGCCATCTCCCTGTTTTAA

Above is displayed the nucleotide sequence of the Acinetobacter baumannii , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 17 nt. 2) Cytosine(C) in the sequence= 14 nt. 3) Guanine(G) in the sequence= 17 nt. 4) Thiamine(T) in the sequence= 19 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 67 nt. 8) CG percentage of the sequence= 46.27% 9) *Melting temperature of the DNA based on the Wallace formula= 73.83oC 10) The entered DNA sequence(5-3) is-67 nt.: GGTAACGTAGGCATCATTAGCCAATACGGCGGTTTTTCAAGGGAGGAATGCCATCTCCCTGTTTTAA 11) The complementary(Com) sequence(3-5) is-67 nt.: CCATTGCATCCGTAGTAATCGGTTATGCCGCCAAAAAGTTCCCTCCTTACGGTAGAGGGACAAAATT 12) The reverse(Rev) sequence(3-5) is-67 nt.: AATTTTGTCCCTCTACCGTAAGGAGGGAACTTTTTGGCGGCATAACCGATTACTACGGATGCAATGG 13) The RevCom sequence(5-3) is-67 nt.: TTAAAACAGGGAGATGGCATTCCTCCCTTGAAAAACCGCCGTATTGGCTAATGATGCCTACGTTACC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-44 nt.: GGTAACGTAGGCATCATTAGCCAATACGGCGGTTTTTCAAGGGA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-44 nt.: TTAAAACAGGGAGATGGCATTCCTCCCTTGAAAAACCGCCGTAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Acinetobacter baumannii , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Acinetobacter baumannii , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -15.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -16.47 kcal/mol. The frequency of the MFE structure in the ensemble is 20.61 %. The ensemble diversity is 4.46. The centroid secondary structure in dot-bracket notation with a minimum free energy of -15.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Acinetobacter baumannii , Fluoride type switch.

2D_Structure (A) (B)

Multiple alignment of the Fluoride type switches

Below is presented the sequences alignment of all the Fluoride type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Fluoride type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Fluoride riboswitches and shorter motifs based on the general one: 1) N{0,9}GGN?GATGGN?GTYCN?CCN{0,3}AACCGCYN{0,7}RGCTGATGACN?YCTRCN{0,9} 2) RGCTGATGAC Motifs identified amongst the Fluoride riboswitches based on the sequences alignment: 1) GCGAACACATCA 2) RSKVRYDHCDYCD Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

The table displays known human pathogenic bacteria bearing the Fluoride type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BA323510

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

Sequence

ATAATCATAGGCGATGGAGTTCGCCATAAACGCTGCTTAGCTAATGACTCCTACCAGTAT

Above is displayed the nucleotide sequence of the Bacillus anthracis , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 18 nt. 2) Cytosine(C) in the sequence= 14 nt. 3) Guanine(G) in the sequence= 12 nt. 4) Thiamine(T) in the sequence= 16 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 60 nt. 8) CG percentage of the sequence= 43.33% 9) *Melting temperature of the DNA based on the Wallace formula= 71.46oC 10) The entered DNA sequence(5-3) is-60 nt.: ATAATCATAGGCGATGGAGTTCGCCATAAACGCTGCTTAGCTAATGACTCCTACCAGTAT 11) The complementary(Com) sequence(3-5) is-60 nt.: TATTAGTATCCGCTACCTCAAGCGGTATTTGCGACGAATCGATTACTGAGGATGGTCATA 12) The reverse(Rev) sequence(3-5) is-60 nt.: TATGACCATCCTCAGTAATCGATTCGTCGCAAATACCGCTTGAGGTAGCGGATACTAATA 13) The RevCom sequence(5-3) is-60 nt.: ATACTGGTAGGAGTCATTAGCTAAGCAGCGTTTATGGCGAACTCCATCGCCTATGATTAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-40 nt.: ATAATCATAGGCGATGGAGTTCGCCATAAACGCTGCTTAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-40 nt.: ATACTGGTAGGAGTCATTAGCTAAGCAGCGTTTATGGCGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -10.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -11.49 kcal/mol. The frequency of the MFE structure in the ensemble is 17.14 %. The ensemble diversity is 7.89. The centroid secondary structure in dot-bracket notation with a minimum free energy of -10.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis , Fluoride type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis , Fluoride type switch.

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

CB224100

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

Sequence

TTATTTGTAGGAGTCATTAGCATTACGCAATTATGGCGAACTCCATCGCCTATATTTAA

Above is displayed the nucleotide sequence of the Clostridium botulinum , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 17 nt. 2) Cytosine(C) in the sequence= 11 nt. 3) Guanine(G) in the sequence= 10 nt. 4) Thiamine(T) in the sequence= 21 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 59 nt. 8) CG percentage of the sequence= 35.59% 9) *Melting temperature of the DNA based on the Wallace formula= 68.10oC 10) The entered DNA sequence(5-3) is-59 nt.: TTATTTGTAGGAGTCATTAGCATTACGCAATTATGGCGAACTCCATCGCCTATATTTAA 11) The complementary(Com) sequence(3-5) is-59 nt.: AATAAACATCCTCAGTAATCGTAATGCGTTAATACCGCTTGAGGTAGCGGATATAAATT 12) The reverse(Rev) sequence(3-5) is-59 nt.: AATTTATATCCGCTACCTCAAGCGGTATTAACGCATTACGATTACTGAGGATGTTTATT 13) The RevCom sequence(5-3) is-59 nt.: TTAAATATAGGCGATGGAGTTCGCCATAATTGCGTAATGCTAATGACTCCTACAAATAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-40 nt.: TTATTTGTAGGAGTCATTAGCATTACGCAATTATGGCGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-40 nt.: TTAAATATAGGCGATGGAGTTCGCCATAATTGCGTAATGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -8.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -10.50 kcal/mol. The frequency of the MFE structure in the ensemble is 3.30 %. The ensemble diversity is 15.4. The centroid secondary structure in dot-bracket notation with a minimum free energy of -7.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum , Fluoride type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum , Fluoride type switch.

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

CD116565

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Clostridium difficile

Length of Switch in nucleotides

Sequence

AATAATTATGGGAATGAGGTTCTCCCTTGGATGATAATATCCTAAACTGCCAATGAGCTGATGACTTCTATGATATC

Above is displayed the nucleotide sequence of the Clostridium difficile , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 24 nt. 2) Cytosine(C) in the sequence= 13 nt. 3) Guanine(G) in the sequence= 15 nt. 4) Thiamine(T) in the sequence= 25 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 77 nt. 8) CG percentage of the sequence= 36.36% 9) *Melting temperature of the DNA based on the Wallace formula= 71.08oC 10) The entered DNA sequence(5-3) is-77 nt.: AATAATTATGGGAATGAGGTTCTCCCTTGGATGATAATATCCTAAACTGCCAATGAGCTGATGACTTCTATGATATC 11) The complementary(Com) sequence(3-5) is-77 nt.: TTATTAATACCCTTACTCCAAGAGGGAACCTACTATTATAGGATTTGACGGTTACTCGACTACTGAAGATACTATAG 12) The reverse(Rev) sequence(3-5) is-77 nt.: CTATAGTATCTTCAGTAGTCGAGTAACCGTCAAATCCTATAATAGTAGGTTCCCTCTTGGAGTAAGGGTATTAATAA 13) The RevCom sequence(5-3) is-77 nt.: GATATCATAGAAGTCATCAGCTCATTGGCAGTTTAGGATATTATCATCCAAGGGAGAACCTCATTCCCATAATTATT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-49 nt.: AATAATTATGGGAATGAGGTTCTCCCTTGGATGATAATATCCTAAACTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-49 nt.: GATATCATAGAAGTCATCAGCTCATTGGCAGTTTAGGATATTATCATCC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium difficile , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium difficile , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -11.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -12.90 kcal/mol. The frequency of the MFE structure in the ensemble is 10.27 %. The ensemble diversity is 11.15. The centroid secondary structure in dot-bracket notation with a minimum free energy of -8.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium difficile , Fluoride type switch.

2D_Structure (A) (B)

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

CP219089

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

Sequence

ATTTTTATAGGCGATGGAGTTCGCCATTAAATGCTTTATGCTAATGACTCCTACAAAATA

Above is displayed the nucleotide sequence of the Clostridium perfringens , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 19 nt. 2) Cytosine(C) in the sequence= 10 nt. 3) Guanine(G) in the sequence= 10 nt. 4) Thiamine(T) in the sequence= 21 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 60 nt. 8) CG percentage of the sequence= 33.33% 9) *Melting temperature of the DNA based on the Wallace formula= 67.36oC 10) The entered DNA sequence(5-3) is-60 nt.: ATTTTTATAGGCGATGGAGTTCGCCATTAAATGCTTTATGCTAATGACTCCTACAAAATA 11) The complementary(Com) sequence(3-5) is-60 nt.: TAAAAATATCCGCTACCTCAAGCGGTAATTTACGAAATACGATTACTGAGGATGTTTTAT 12) The reverse(Rev) sequence(3-5) is-60 nt.: ATAAAACATCCTCAGTAATCGTATTTCGTAAATTACCGCTTGAGGTAGCGGATATTTTTA 13) The RevCom sequence(5-3) is-60 nt.: TATTTTGTAGGAGTCATTAGCATAAAGCATTTAATGGCGAACTCCATCGCCTATAAAAAT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-40 nt.: ATTTTTATAGGCGATGGAGTTCGCCATTAAATGCTTTATG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-40 nt.: TATTTTGTAGGAGTCATTAGCATAAAGCATTTAATGGCGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -10.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -11.03 kcal/mol. The frequency of the MFE structure in the ensemble is 26.06 %. The ensemble diversity is 7.04 . The centroid secondary structure in dot-bracket notation with a minimum free energy of -9.50 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens , Fluoride type switch.

2D_Structure (A) (B)

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

EF445098

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Enterococcus faecalis

Length of Switch in nucleotides

Sequence

TCTCTAGTAGGCGTCATTAGCTGTCTTTCGATCAACGTTTAAAGGCGAACACCATCACCTTATTCCTT

Above is displayed the nucleotide sequence of the Enterococcus faecalis , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 16 nt. 2) Cytosine(C) in the sequence= 18 nt. 3) Guanine(G) in the sequence= 11 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 68 nt. 8) CG percentage of the sequence= 42.65% 9) *Melting temperature of the DNA based on the Wallace formula= 72.50oC 10) The entered DNA sequence(5-3) is-68 nt.: TCTCTAGTAGGCGTCATTAGCTGTCTTTCGATCAACGTTTAAAGGCGAACACCATCACCTTATTCCTT 11) The complementary(Com) sequence(3-5) is-68 nt.: AGAGATCATCCGCAGTAATCGACAGAAAGCTAGTTGCAAATTTCCGCTTGTGGTAGTGGAATAAGGAA 12) The reverse(Rev) sequence(3-5) is-68 nt.: TTCCTTATTCCACTACCACAAGCGGAAATTTGCAACTAGCTTTCTGTCGATTACTGCGGATGATCTCT 13) The RevCom sequence(5-3) is-68 nt.: AAGGAATAAGGTGATGGTGTTCGCCTTTAAACGTTGATCGAAAGACAGCTAATGACGCCTACTAGAGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-44 nt.: TCTCTAGTAGGCGTCATTAGCTGTCTTTCGATCAACGTTTAAAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-44 nt.: AAGGAATAAGGTGATGGTGTTCGCCTTTAAACGTTGATCGAAAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecalis , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecalis , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -9.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -9.90 kcal/mol. The frequency of the MFE structure in the ensemble is 23.12 %. The ensemble diversity is 9.67. The centroid secondary structure in dot-bracket notation with a minimum free energy of -8.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecalis , Fluoride type switch.

2D_Structure (A) (B)

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

EF891080

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Enterococcus faecium

Length of Switch in nucleotides

Sequence

ACTTTAGTAGGCGTCATTAGCTATCTTTCGTTAGCATTTAAAGGCGAACACCATCACCTATTCACTT

Above is displayed the nucleotide sequence of the Enterococcus faecium , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 18 nt. 2) Cytosine(C) in the sequence= 16 nt. 3) Guanine(G) in the sequence= 10 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 67 nt. 8) CG percentage of the sequence= 38.81% 9) *Melting temperature of the DNA based on the Wallace formula= 70.77oC 10) The entered DNA sequence(5-3) is-67 nt.: ACTTTAGTAGGCGTCATTAGCTATCTTTCGTTAGCATTTAAAGGCGAACACCATCACCTATTCACTT 11) The complementary(Com) sequence(3-5) is-67 nt.: TGAAATCATCCGCAGTAATCGATAGAAAGCAATCGTAAATTTCCGCTTGTGGTAGTGGATAAGTGAA 12) The reverse(Rev) sequence(3-5) is-67 nt.: TTCACTTATCCACTACCACAAGCGGAAATTTACGATTGCTTTCTATCGATTACTGCGGATGATTTCA 13) The RevCom sequence(5-3) is-67 nt.: AAGTGAATAGGTGATGGTGTTCGCCTTTAAATGCTAACGAAAGATAGCTAATGACGCCTACTAAAGT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-44 nt.: ACTTTAGTAGGCGTCATTAGCTATCTTTCGTTAGCATTTAAAGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-44 nt.: AAGTGAATAGGTGATGGTGTTCGCCTTTAAATGCTAACGAAAGA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Enterococcus faecium , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Enterococcus faecium , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -10.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -10.50 kcal/mol. The frequency of the MFE structure in the ensemble is 44.34 %. The ensemble diversity is 3.40. The centroid secondary structure in dot-bracket notation with a minimum free energy of -10.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Enterococcus faecium , Fluoride type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Enterococcus faecium , Fluoride type switch.

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

KP650197

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Klebsiella pneumoniae

Length of Switch in nucleotides

Sequence

TTGCGGCGAGGTGATGGCGTTCCACCTTACCCAACCGCTTCCCCTGAGAAGCTGATGACGCCTGATATTAC

Above is displayed the nucleotide sequence of the Klebsiella pneumoniae , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 14 nt. 2) Cytosine(C) in the sequence= 22 nt. 3) Guanine(G) in the sequence= 18 nt. 4) Thiamine(T) in the sequence= 17 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 71 nt. 8) CG percentage of the sequence= 56.34% 9) *Melting temperature of the DNA based on the Wallace formula= 78.53oC 10) The entered DNA sequence(5-3) is-71 nt.: TTGCGGCGAGGTGATGGCGTTCCACCTTACCCAACCGCTTCCCCTGAGAAGCTGATGACGCCTGATATTAC 11) The complementary(Com) sequence(3-5) is-71 nt.: AACGCCGCTCCACTACCGCAAGGTGGAATGGGTTGGCGAAGGGGACTCTTCGACTACTGCGGACTATAATG 12) The reverse(Rev) sequence(3-5) is-71 nt.: CATTATAGTCCGCAGTAGTCGAAGAGTCCCCTTCGCCAACCCATTCCACCTTGCGGTAGTGGAGCGGCGTT 13) The RevCom sequence(5-3) is-71 nt.: GTAATATCAGGCGTCATCAGCTTCTCAGGGGAAGCGGTTGGGTAAGGTGGAACGCCATCACCTCGCCGCAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-46 nt.: TTGCGGCGAGGTGATGGCGTTCCACCTTACCCAACCGCTTCCCCTG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-46 nt.: GTAATATCAGGCGTCATCAGCTTCTCAGGGGAAGCGGTTGGGTAAG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Klebsiella pneumoniae , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Klebsiella pneumoniae , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -16.50 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -18.01 kcal/mol. The frequency of the MFE structure in the ensemble is 8.62 %. The ensemble diversity is 14.59. The centroid secondary structure in dot-bracket notation with a minimum free energy of -10.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Klebsiella pneumoniae , Fluoride type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Klebsiella pneumoniae , Fluoride type switch.

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

PA320584

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Pseudomonas aeruginosa

Length of Switch in nucleotides

Sequence

TCATGCGTAGGCATCATCAGCCCCAGGGGCGGTTGAAGGAGGAATGCCATCTCCTGTCGGCAA

Above is displayed the nucleotide sequence of the Pseudomonas aeruginosa , Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 14 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 20 nt. 4) Thiamine(T) in the sequence= 12 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 63 nt. 8) CG percentage of the sequence= 58.73% 9) *Melting temperature of the DNA based on the Wallace formula= 78.31oC 10) The entered DNA sequence(5-3) is-63 nt.: TCATGCGTAGGCATCATCAGCCCCAGGGGCGGTTGAAGGAGGAATGCCATCTCCTGTCGGCAA 11) The complementary(Com) sequence(3-5) is-63 nt.: AGTACGCATCCGTAGTAGTCGGGGTCCCCGCCAACTTCCTCCTTACGGTAGAGGACAGCCGTT 12) The reverse(Rev) sequence(3-5) is-63 nt.: AACGGCTGTCCTCTACCGTAAGGAGGAAGTTGGCGGGGACCCCGACTACTACGGATGCGTACT 13) The RevCom sequence(5-3) is-63 nt.: TTGCCGACAGGAGATGGCATTCCTCCTTCAACCGCCCCTGGGGCTGATGATGCCTACGCATGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-42 nt.: TCATGCGTAGGCATCATCAGCCCCAGGGGCGGTTGAAGGAGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-42 nt.: TTGCCGACAGGAGATGGCATTCCTCCTTCAACCGCCCCTGGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Pseudomonas aeruginosa , Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Pseudomonas aeruginosa , Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -20.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -20.76 kcal/mol. The frequency of the MFE structure in the ensemble is 28.98 %. The ensemble diversity is 5.53. The centroid secondary structure in dot-bracket notation with a minimum free energy of -20.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Pseudomonas aeruginosa , Fluoride type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Pseudomonas aeruginosa , Fluoride type switch.

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

YP587908

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RiboSwitch type

Fluoride type switch

Bacteria strain target

Yersinia pestis

Length of Switch in nucleotides

Sequence

GGTCACGTAGACATCATTAGCCTTGTTAGGGCGGTTATGGAGGCGTGTCATCTCCAGATCTTGA

Above is displayed the nucleotide sequence of the Yersinia pestis, Fluoride type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 13 nt. 2) Cytosine(C) in the sequence= 13 nt. 3) Guanine(G) in the sequence= 19 nt. 4) Thiamine(T) in the sequence= 19 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 64 nt. 8) CG percentage of the sequence= 50.00% 9) *Melting temperature of the DNA based on the Wallace formula= 74.89oC 10) The entered DNA sequence(5-3) is-64 nt.: GGTCACGTAGACATCATTAGCCTTGTTAGGGCGGTTATGGAGGCGTGTCATCTCCAGATCTTGA 11) The complementary(Com) sequence(3-5) is-64 nt.: CCAGTGCATCTGTAGTAATCGGAACAATCCCGCCAATACCTCCGCACAGTAGAGGTCTAGAACT 12) The reverse(Rev) sequence(3-5) is-64 nt.: AGTTCTAGACCTCTACTGTGCGGAGGTATTGGCGGGATTGTTCCGATTACTACAGATGCACTGG 13) The RevCom sequence(5-3) is-64 nt.: TCAAGATCTGGAGATGACACGCCTCCATAACCGCCCTAACAAGGCTAATGATGTCTACGTGACC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-42 nt.: GGTCACGTAGACATCATTAGCCTTGTTAGGGCGGTTATGGAG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-42 nt.: TCAAGATCTGGAGATGACACGCCTCCATAACCGCCCTAACAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Yersinia pestis, Fluoride type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Yersinia pestis, Fluoride type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -14.60 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -16.29 kcal/mol. The frequency of the MFE structure in the ensemble is 6.43 %. The ensemble diversity is 14.42. The centroid secondary structure in dot-bracket notation with a minimum free energy of -13.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Yersinia pestis, Fluoride type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Yersinia pestis, Fluoride type switch.

Multiple alignment of the Fluoride type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Fluoride type switches involved in.

Multi_resistance strains for the Fluoride type switches

RiboSwitch_ID:

AB775671

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RiboSwitch type

Glycine type switch

Bacteria strain target

Acinetobacter baumannii

Length of Switch in nucleotides

Sequence

AAAATTATTGCGGGAGAGAGGTTCTTAAGAACCCGCCGAAGGAGCAACAGGCCCGGAAACTCTCAGGCAAAAGGACTGTAATAATTAA

Above is displayed the nucleotide sequence of the Acinetobacter baumannii, Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 17 nt. 3) Guanine(G) in the sequence= 23 nt. 4) Thiamine(T) in the sequence= 15 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 88 nt. 8) CG percentage of the sequence= 45.45% 9) *Melting temperature of the DNA based on the Wallace formula= 75.90oC 10) The entered DNA sequence(5-3) is-88 nt.: AAAATTATTGCGGGAGAGAGGTTCTTAAGAACCCGCCGAAGGAGCAACAGGCCCGGAAACTCTCAGGCAAAAGGACTGTAATAATTAA 11) The complementary(Com) sequence(3-5) is-88 nt.: TTTTAATAACGCCCTCTCTCCAAGAATTCTTGGGCGGCTTCCTCGTTGTCCGGGCCTTTGAGAGTCCGTTTTCCTGACATTATTAATT 12) The reverse(Rev) sequence(3-5) is-88 nt.: AATTAATAATGTCAGGAAAACGGACTCTCAAAGGCCCGGACAACGAGGAAGCCGCCCAAGAATTCTTGGAGAGAGGGCGTTATTAAAA 13) The RevCom sequence(5-3) is-88 nt.: TTAATTATTACAGTCCTTTTGCCTGAGAGTTTCCGGGCCTGTTGCTCCTTCGGCGGGTTCTTAAGAACCTCTCTCCCGCAATAATTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-54 nt.: AAAATTATTGCGGGAGAGAGGTTCTTAAGAACCCGCCGAAGGAGCAACAGGCCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-54 nt.: TTAATTATTACAGTCCTTTTGCCTGAGAGTTTCCGGGCCTGTTGCTCCTTCGGC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Acinetobacter baumannii, Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Acinetobacter baumannii, Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -20.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -22.06 kcal/mol. The frequency of the MFE structure in the ensemble is 12.94 %. The ensemble diversity is 12.56. The centroid secondary structure in dot-bracket notation with a minimum free energy of -15.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Acinetobacter baumannii, Glycine type switch.

2D_Structure (A) (B)

Multiple alignment of the Glycine type switches

Below is presented the sequences alignment of all the Glycine type switches currently present in the Rswitch database. In the alignment the consensus sequence is displayed and conserved regions amongst the sequences are highlighted. Less conserved nucleotides are also depicted and marked in squares.

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The consensus sequence (general motif) of the Glycine type switch is presented below followed by motifs generated based on the consensus sequence. Moreover motifs extracted from the sequences alignment presented above in the "Multiple alignment" section are presented.

Below are shown the general motif sequence of the Glycine riboswitches and shorter motifs based on the general one: 1) N{0,10}CN?GGAGAGN{0,10}RN{0,7}CRCCGAGRGYAAR{0,12}AAN?CTCTCGGYN{0,4}RGACN?GN{0,10} 2) CRCCGAGRGYAAR Key: --> N{0,4} = Non, or up to 4 nucleotides can be present --> N? = Non or 1 nucleotide can be present

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

The table displays known human pathogenic bacteria bearing the Glycine type switches. It includes the resistance of these pathogens to currently available drugs. The first column provides the name of the Human Bacterial Pathogen (HBP). The second one indicates with a plus (+) symbol the presence of the riboswitch in the particular bacterium. The third column indicates the resistance with a (+) symbol to the Antiretroviral (AR) drug classes that are displayed in the last column. In the HBP column, priority pathogens for the World Health Organisation are depicted in pink-filled box.

RiboSwitch_ID:

BA118680

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RiboSwitch type

Glycine type switch

Bacteria strain target

Bacillus anthracis

Length of Switch in nucleotides

119

Sequence

CGCTTGTCTCTGTCCTTTTACCTGAGAGATTATCCGCTATAGTAGCGGATTTGCTCCTTCGGTGCTCGTTTTCCTCTACGCTATTTAAAGCGAGAGGGAGTCTCTCCAGAGATTCGTCC

Above is displayed the nucleotide sequence of the Bacillus anthracis , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 31 nt. 3) Guanine(G) in the sequence= 27 nt. 4) Thiamine(T) in the sequence= 41 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 119 nt. 8) CG percentage of the sequence= 48.74% 9) *Melting temperature of the DNA based on the Wallace formula= 79.23oC 10) The entered DNA sequence(5-3) is-119 nt.: CGCTTGTCTCTGTCCTTTTACCTGAGAGATTATCCGCTATAGTAGCGGATTTGCTCCTTCGGTGCTCGTTTTCCTCTACGCTATTTAAAGCGAGAGGGAGTCTCTCCAGAGATTCGTCC 11) The complementary(Com) sequence(3-5) is-119 nt.: GCGAACAGAGACAGGAAAATGGACTCTCTAATAGGCGATATCATCGCCTAAACGAGGAAGCCACGAGCAAAAGGAGATGCGATAAATTTCGCTCTCCCTCAGAGAGGTCTCTAAGCAGG 12) The reverse(Rev) sequence(3-5) is-119 nt.: CCTGCTTAGAGACCTCTCTGAGGGAGAGCGAAATTTATCGCATCTCCTTTTGCTCGTGGCTTCCTCGTTTAGGCGATGATATCGCCTATTAGAGAGTCCATTTTCCTGTCTCTGTTCGC 13) The RevCom sequence(5-3) is-119 nt.: GGACGAATCTCTGGAGAGACTCCCTCTCGCTTTAAATAGCGTAGAGGAAAACGAGCACCGAAGGAGCAAATCCGCTACTATAGCGGATAATCTCTCAGGTAAAAGGACAGAGACAAGCG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-70 nt.: CGCTTGTCTCTGTCCTTTTACCTGAGAGATTATCCGCTATAGTAGCGGATTTGCTCCTTCGGTGCTCGTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-70 nt.: GGACGAATCTCTGGAGAGACTCCCTCTCGCTTTAAATAGCGTAGAGGAAAACGAGCACCGAAGGAGCAAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bacillus anthracis , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bacillus anthracis , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -42.80 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -44.27 kcal/mol. The frequency of the MFE structure in the ensemble is 9.21 %. The ensemble diversity is 8.69. The centroid secondary structure in dot-bracket notation with a minimum free energy of -41.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bacillus anthracis , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bacillus anthracis , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

BP827460

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RiboSwitch type

Glycine type switch

Bacteria strain target

Bordetella pertussis

Length of Switch in nucleotides

120

Sequence

AAACAGCACTCTGGAGAGACCTGGCGCGGCCACCTTCGCGGTGCGCAAGCAGCCCAGGCGCCGAAGGTGCAAACCCGCTCGCGCGGGGCAACTCTCAGGCAAAAGGACAGAGGGGCGGAA

Above is displayed the nucleotide sequence of the Bordetella pertussis , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 30 nt. 2) Cytosine(C) in the sequence= 38 nt. 3) Guanine(G) in the sequence= 42 nt. 4) Thiamine(T) in the sequence= 10 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 120 nt. 8) CG percentage of the sequence= 66.67% 9) *Melting temperature of the DNA based on the Wallace formula= 86.63oC 10) The entered DNA sequence(5-3) is-120 nt.: AAACAGCACTCTGGAGAGACCTGGCGCGGCCACCTTCGCGGTGCGCAAGCAGCCCAGGCGCCGAAGGTGCAAACCCGCTCGCGCGGGGCAACTCTCAGGCAAAAGGACAGAGGGGCGGAA 11) The complementary(Com) sequence(3-5) is-120 nt.: TTTGTCGTGAGACCTCTCTGGACCGCGCCGGTGGAAGCGCCACGCGTTCGTCGGGTCCGCGGCTTCCACGTTTGGGCGAGCGCGCCCCGTTGAGAGTCCGTTTTCCTGTCTCCCCGCCTT 12) The reverse(Rev) sequence(3-5) is-120 nt.: AAGGCGGGGAGACAGGAAAACGGACTCTCAACGGGGCGCGCTCGCCCAAACGTGGAAGCCGCGGACCCGACGAACGCGTGGCGCTTCCACCGGCGCGGTCCAGAGAGGTCTCACGACAAA 13) The RevCom sequence(5-3) is-120 nt.: TTCCGCCCCTCTGTCCTTTTGCCTGAGAGTTGCCCCGCGCGAGCGGGTTTGCACCTTCGGCGCCTGGGCTGCTTGCGCACCGCGAAGGTGGCCGCGCCAGGTCTCTCCAGAGTGCTGTTT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-70 nt.: AAACAGCACTCTGGAGAGACCTGGCGCGGCCACCTTCGCGGTGCGCAAGCAGCCCAGGCGCCGAAGGTGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-70 nt.: TTCCGCCCCTCTGTCCTTTTGCCTGAGAGTTGCCCCGCGCGAGCGGGTTTGCACCTTCGGCGCCTGGGCT ?

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Bordetella pertussis , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Bordetella pertussis , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -47.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -48.49 kcal/mol. The frequency of the MFE structure in the ensemble is 12.23 %. The ensemble diversity is 11.61. The centroid secondary structure in dot-bracket notation with a minimum free energy of -44.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Bordetella pertussis , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Bordetella pertussis , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

BMA16542

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RiboSwitch type

Glycine type switch

Bacteria strain target

Brucella melitensis Abortus

Length of Switch in nucleotides

Sequence

TGTCTGTTTGCGGGAGAGAGCCGTTAAGGCCGCCGAAGGGGAAAACGCCCGAAATCTCTCAGGTACAAGGAACCGCAGGCGGGTA

Above is displayed the nucleotide sequence of the Brucella melitensis Abortus , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 22 nt. 2) Cytosine(C) in the sequence= 20 nt. 3) Guanine(G) in the sequence= 30 nt. 4) Thiamine(T) in the sequence= 13 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 85 nt. 8) CG percentage of the sequence= 58.82% 9) *Melting temperature of the DNA based on the Wallace formula= 81.11oC 10) The entered DNA sequence(5-3) is-85 nt.: TGTCTGTTTGCGGGAGAGAGCCGTTAAGGCCGCCGAAGGGGAAAACGCCCGAAATCTCTCAGGTACAAGGAACCGCAGGCGGGTA 11) The complementary(Com) sequence(3-5) is-85 nt.: ACAGACAAACGCCCTCTCTCGGCAATTCCGGCGGCTTCCCCTTTTGCGGGCTTTAGAGAGTCCATGTTCCTTGGCGTCCGCCCAT 12) The reverse(Rev) sequence(3-5) is-85 nt.: ATGGGCGGACGCCAAGGAACATGGACTCTCTAAAGCCCGCAAAAGGGGAAGCCGCCGGAATTGCCGAGAGAGGGCGTTTGTCTGT 13) The RevCom sequence(5-3) is-85 nt.: TACCCGCCTGCGGTTCCTTGTACCTGAGAGATTTCGGGCGTTTTCCCCTTCGGCGGCCTTAACGGCTCTCTCCCGCAAACAGACA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-53 nt.: TGTCTGTTTGCGGGAGAGAGCCGTTAAGGCCGCCGAAGGGGAAAACGCCCGAA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-53 nt.: TACCCGCCTGCGGTTCCTTGTACCTGAGAGATTTCGGGCGTTTTCCCCTTCGG

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Brucella melitensis Abortus , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Brucella melitensis Abortus , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -28.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -29.56 kcal/mol. The frequency of the MFE structure in the ensemble is 15.29 %. The ensemble diversity is 6.13. The centroid secondary structure in dot-bracket notation with a minimum free energy of -23.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Brucella melitensis Abortus , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Brucella melitensis Abortus , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

CB111542

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RiboSwitch type

Glycine type switch

Bacteria strain target

Clostridium botulinum

Length of Switch in nucleotides

100

Sequence

GGACGAGCCTCTGGAGAGACTCATATTTATTATGAGCACCGAAGGAGCAAGGCAAATTTTATTTGCTGAAACTCTCAGGTAAAAGGACAGGGGATAGGAT

Above is displayed the nucleotide sequence of the Clostridium botulinum , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 16 nt. 3) Guanine(G) in the sequence= 28 nt. 4) Thiamine(T) in the sequence= 23 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 100 nt. 8) CG percentage of the sequence= 44.00% 9) *Melting temperature of the DNA based on the Wallace formula= 76.22oC 10) The entered DNA sequence(5-3) is-100 nt.: GGACGAGCCTCTGGAGAGACTCATATTTATTATGAGCACCGAAGGAGCAAGGCAAATTTTATTTGCTGAAACTCTCAGGTAAAAGGACAGGGGATAGGAT 11) The complementary(Com) sequence(3-5) is-100 nt.: CCTGCTCGGAGACCTCTCTGAGTATAAATAATACTCGTGGCTTCCTCGTTCCGTTTAAAATAAACGACTTTGAGAGTCCATTTTCCTGTCCCCTATCCTA 12) The reverse(Rev) sequence(3-5) is-100 nt.: TAGGATAGGGGACAGGAAAATGGACTCTCAAAGTCGTTTATTTTAAACGGAACGAGGAAGCCACGAGTATTATTTATACTCAGAGAGGTCTCCGAGCAGG 13) The RevCom sequence(5-3) is-100 nt.: ATCCTATCCCCTGTCCTTTTACCTGAGAGTTTCAGCAAATAAAATTTGCCTTGCTCCTTCGGTGCTCATAATAAATATGAGTCTCTCCAGAGGCTCGTCC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: GGACGAGCCTCTGGAGAGACTCATATTTATTATGAGCACCGAAGGAGCAAGGCAAATTTT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: ATCCTATCCCCTGTCCTTTTACCTGAGAGTTTCAGCAAATAAAATTTGCCTTGCTCCTTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium botulinum , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium botulinum , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -25.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -25.86 kcal/mol. The frequency of the MFE structure in the ensemble is 47.75 %. The ensemble diversity is 2.39. The centroid secondary structure in dot-bracket notation with a minimum free energy of -25.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium botulinum , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Clostridium botulinum , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

CP710253

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RiboSwitch type

Glycine type switch

Bacteria strain target

Clostridium perfringens

Length of Switch in nucleotides

Sequence

ACCTTATCCTCTGTCCTTTTACCTGAGAGTTTCAGTCAAAAAATTTGACCTTGCTCCTTCGGTGCTCTTTTTTAAAAGAGTCTCTCCAGAGGCTCGTCC

Above is displayed the nucleotide sequence of the Clostridium perfringens , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 16 nt. 4) Thiamine(T) in the sequence= 36 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 99 nt. 8) CG percentage of the sequence= 43.43% 9) *Melting temperature of the DNA based on the Wallace formula= 75.92oC 10) The entered DNA sequence(5-3) is-99 nt.: ACCTTATCCTCTGTCCTTTTACCTGAGAGTTTCAGTCAAAAAATTTGACCTTGCTCCTTCGGTGCTCTTTTTTAAAAGAGTCTCTCCAGAGGCTCGTCC 11) The complementary(Com) sequence(3-5) is-99 nt.: TGGAATAGGAGACAGGAAAATGGACTCTCAAAGTCAGTTTTTTAAACTGGAACGAGGAAGCCACGAGAAAAAATTTTCTCAGAGAGGTCTCCGAGCAGG 12) The reverse(Rev) sequence(3-5) is-99 nt.: CCTGCTCGGAGACCTCTCTGAGAAAATTTTTTCTCGTGGCTTCCTCGTTCCAGTTTAAAAAACTGACTTTGAGAGTCCATTTTCCTGTCTCCTATTCCA 13) The RevCom sequence(5-3) is-99 nt.: GGACGAGCCTCTGGAGAGACTCTTTTAAAAAAGAGCACCGAAGGAGCAAGGTCAAATTTTTTGACTGAAACTCTCAGGTAAAAGGACAGAGGATAAGGT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: ACCTTATCCTCTGTCCTTTTACCTGAGAGTTTCAGTCAAAAAATTTGACCTTGCTCCTTC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: GGACGAGCCTCTGGAGAGACTCTTTTAAAAAAGAGCACCGAAGGAGCAAGGTCAAATTTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium perfringens , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium perfringens , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -23.40 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -25.11 kcal/mol. The frequency of the MFE structure in the ensemble is 6.23 %. The ensemble diversity is 7.34. The centroid secondary structure in dot-bracket notation with a minimum free energy of -23.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium perfringens , Glycine type switch.

2D_Structure (A) (B)

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

CTE88753

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RiboSwitch type

Glycine type switch

Bacteria strain target

Clostridium tetani E88

Length of Switch in nucleotides

100

Sequence

CTTCTACGCTCTGTCCTTTTACCTGAGAGTTTCATTGGTTTTACCCAACTTGCTCCTTCGGTGCTCTTTTATAAAAAAGAGTCTCTCCAGAGTTTCGTCC

Above is displayed the nucleotide sequence of the Clostridium tetani E88 , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 18 nt. 2) Cytosine(C) in the sequence= 27 nt. 3) Guanine(G) in the sequence= 16 nt. 4) Thiamine(T) in the sequence= 39 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 100 nt. 8) CG percentage of the sequence= 43.00% 9) *Melting temperature of the DNA based on the Wallace formula= 75.81oC 10) The entered DNA sequence(5-3) is-100 nt.: CTTCTACGCTCTGTCCTTTTACCTGAGAGTTTCATTGGTTTTACCCAACTTGCTCCTTCGGTGCTCTTTTATAAAAAAGAGTCTCTCCAGAGTTTCGTCC 11) The complementary(Com) sequence(3-5) is-100 nt.: GAAGATGCGAGACAGGAAAATGGACTCTCAAAGTAACCAAAATGGGTTGAACGAGGAAGCCACGAGAAAATATTTTTTCTCAGAGAGGTCTCAAAGCAGG 12) The reverse(Rev) sequence(3-5) is-100 nt.: CCTGCTTTGAGACCTCTCTGAGAAAAAATATTTTCTCGTGGCTTCCTCGTTCAACCCATTTTGGTTACTTTGAGAGTCCATTTTCCTGTCTCGCATCTTC 13) The RevCom sequence(5-3) is-100 nt.: GGACGAAACTCTGGAGAGACTCTTTTTTATAAAAGAGCACCGAAGGAGCAAGTTGGGTAAAACCAATGAAACTCTCAGGTAAAAGGACAGAGCGTAGAAG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: CTTCTACGCTCTGTCCTTTTACCTGAGAGTTTCATTGGTTTTACCCAACTTGCTCCTTCG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: GGACGAAACTCTGGAGAGACTCTTTTTTATAAAAGAGCACCGAAGGAGCAAGTTGGGTAA

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Clostridium tetani E88 , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Clostridium tetani E88 , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.52 kcal/mol. The frequency of the MFE structure in the ensemble is 8.55 %. The ensemble diversity is 7.48. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.00 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Clostridium tetani E88 , Glycine type switch.

2D_Structure (A) (B)

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

HI612321

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RiboSwitch type

Glycine type switch

Bacteria strain target

Haemophilus influenzae

Length of Switch in nucleotides

110

Sequence

TCTTTTGCCCCTGTCCTTTTGCCTGAGCGTTTGAAAAACGATTGAAAAATTAACCGCTCTTTTGCGCTTCGGCGTCCATTTCTAAAATGGATCTCTCCAAGGGTTCGTCC

Above is displayed the nucleotide sequence of the Haemophilus influenzae , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 22 nt. 2) Cytosine(C) in the sequence= 29 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 38 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 110 nt. 8) CG percentage of the sequence= 45.45% 9) *Melting temperature of the DNA based on the Wallace formula= 77.42oC 10) The entered DNA sequence(5-3) is-110 nt.: TCTTTTGCCCCTGTCCTTTTGCCTGAGCGTTTGAAAAACGATTGAAAAATTAACCGCTCTTTTGCGCTTCGGCGTCCATTTCTAAAATGGATCTCTCCAAGGGTTCGTCC 11) The complementary(Com) sequence(3-5) is-110 nt.: AGAAAACGGGGACAGGAAAACGGACTCGCAAACTTTTTGCTAACTTTTTAATTGGCGAGAAAACGCGAAGCCGCAGGTAAAGATTTTACCTAGAGAGGTTCCCAAGCAGG 12) The reverse(Rev) sequence(3-5) is-110 nt.: CCTGCTTGGGAACCTCTCTAGGTAAAATCTTTACCTGCGGCTTCGCGTTTTCTCGCCAATTAAAAAGTTAGCAAAAAGTTTGCGAGTCCGTTTTCCTGTCCCCGTTTTCT 13) The RevCom sequence(5-3) is-110 nt.: GGACGAACCCTTGGAGAGATCCATTTTAGAAATGGACGCCGAAGCGCAAAAGAGCGGTTAATTTTTCAATCGTTTTTCAAACGCTCAGGCAAAAGGACAGGGGCAAAAGA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-65 nt.: TCTTTTGCCCCTGTCCTTTTGCCTGAGCGTTTGAAAAACGATTGAAAAATTAACCGCTCTTTTGC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-65 nt.: GGACGAACCCTTGGAGAGATCCATTTTAGAAATGGACGCCGAAGCGCAAAAGAGCGGTTAATTTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Haemophilus influenzae , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Haemophilus influenzae , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -25.00 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -26.91 kcal/mol. The frequency of the MFE structure in the ensemble is 4.49 %. The ensemble diversity is 11.48. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.90 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Haemophilus influenzae , Glycine type switch.

2D_Structure (A) (B)

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

LM659801

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RiboSwitch type

Glycine type switch

Bacteria strain target

Listeria monocytogenes

Length of Switch in nucleotides

Sequence

GTGAATGTAAGCAGAGAGACTGCGAAAAGCAGCGCCGACGGGGAAAGCATATATTATGTGAAACTCTCAGGCAAAAGGATGTTTACGGGACG

Above is displayed the nucleotide sequence of the Listeria monocytogenes , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 32 nt. 2) Cytosine(C) in the sequence= 15 nt. 3) Guanine(G) in the sequence= 29 nt. 4) Thiamine(T) in the sequence= 16 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 92 nt. 8) CG percentage of the sequence= 47.83% 9) *Melting temperature of the DNA based on the Wallace formula= 77.20oC 10) The entered DNA sequence(5-3) is-92 nt.: GTGAATGTAAGCAGAGAGACTGCGAAAAGCAGCGCCGACGGGGAAAGCATATATTATGTGAAACTCTCAGGCAAAAGGATGTTTACGGGACG 11) The complementary(Com) sequence(3-5) is-92 nt.: CACTTACATTCGTCTCTCTGACGCTTTTCGTCGCGGCTGCCCCTTTCGTATATAATACACTTTGAGAGTCCGTTTTCCTACAAATGCCCTGC 12) The reverse(Rev) sequence(3-5) is-92 nt.: GCAGGGCATTTGTAGGAAAACGGACTCTCAAAGTGTATTATATACGAAAGGGGCAGCCGCGACGAAAAGCGTCAGAGAGACGAATGTAAGTG 13) The RevCom sequence(5-3) is-92 nt.: CGTCCCGTAAACATCCTTTTGCCTGAGAGTTTCACATAATATATGCTTTCCCCGTCGGCGCTGCTTTTCGCAGTCTCTCTGCTTACATTCAC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-56 nt.: GTGAATGTAAGCAGAGAGACTGCGAAAAGCAGCGCCGACGGGGAAAGCATATATTA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-56 nt.: CGTCCCGTAAACATCCTTTTGCCTGAGAGTTTCACATAATATATGCTTTCCCCGTC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Listeria monocytogenes , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Listeria monocytogenes , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -22.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.86 kcal/mol. The frequency of the MFE structure in the ensemble is 21.22 %. The ensemble diversity is 6.98. The centroid secondary structure in dot-bracket notation with a minimum free energy of -22.60 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Listeria monocytogenes , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Listeria monocytogenes , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

MT007871

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RiboSwitch type

Glycine type switch

Bacteria strain target

Mycobacterium tuberculosis

Length of Switch in nucleotides

Sequence

CGCTCTAGTGCGGGAGAGTTCTGTGGCTGCCAGCTACGGACGCCGAAGGAGCAATACCTCTCCGTCAACCTCTCAGGCACCCGGACCGCGCGAGACTA

Above is displayed the nucleotide sequence of the Mycobacterium tuberculosis , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 20 nt. 2) Cytosine(C) in the sequence= 33 nt. 3) Guanine(G) in the sequence= 29 nt. 4) Thiamine(T) in the sequence= 16 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 98 nt. 8) CG percentage of the sequence= 63.27% 9) *Melting temperature of the DNA based on the Wallace formula= 83.98oC 10) The entered DNA sequence(5-3) is-98 nt.: CGCTCTAGTGCGGGAGAGTTCTGTGGCTGCCAGCTACGGACGCCGAAGGAGCAATACCTCTCCGTCAACCTCTCAGGCACCCGGACCGCGCGAGACTA 11) The complementary(Com) sequence(3-5) is-98 nt.: GCGAGATCACGCCCTCTCAAGACACCGACGGTCGATGCCTGCGGCTTCCTCGTTATGGAGAGGCAGTTGGAGAGTCCGTGGGCCTGGCGCGCTCTGAT 12) The reverse(Rev) sequence(3-5) is-98 nt.: ATCAGAGCGCGCCAGGCCCACGGACTCTCCAACTGCCTCTCCATAACGAGGAAGCCGCAGGCATCGACCGTCGGTGTCTTGAGAGGGCGTGATCTCGC 13) The RevCom sequence(5-3) is-98 nt.: TAGTCTCGCGCGGTCCGGGTGCCTGAGAGGTTGACGGAGAGGTATTGCTCCTTCGGCGTCCGTAGCTGGCAGCCACAGAACTCTCCCGCACTAGAGCG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-59 nt.: CGCTCTAGTGCGGGAGAGTTCTGTGGCTGCCAGCTACGGACGCCGAAGGAGCAATACCT 15) The RevCom sequence(5-3) to order a 10nt overlapping region-59 nt.: TAGTCTCGCGCGGTCCGGGTGCCTGAGAGGTTGACGGAGAGGTATTGCTCCTTCGGCGT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Mycobacterium tuberculosis , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Mycobacterium tuberculosis , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -32.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -33.75 kcal/mol. The frequency of the MFE structure in the ensemble is 6.87 %. The ensemble diversity is 23.03. The centroid secondary structure in dot-bracket notation with a minimum free energy of -29.30 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Mycobacterium tuberculosis , Glycine type switch.

2D_Structure (A) (B)

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

NM636850

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RiboSwitch type

Glycine type switch

Bacteria strain target

Neisseria meningitidis

Length of Switch in nucleotides

Sequence

GGGAAATGTGCAGGAGAGTGTTACACCCAACTACAATGTAACCACCGAAGGCGCAGACACCCTTAAATCGCTCAGGTATCAGGGACTGCACATTGAAA

Above is displayed the nucleotide sequence of the Neisseria meningitidis , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 33 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 24 nt. 4) Thiamine(T) in the sequence= 17 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 98 nt. 8) CG percentage of the sequence= 48.98% 9) *Melting temperature of the DNA based on the Wallace formula= 78.12oC 10) The entered DNA sequence(5-3) is-98 nt.: GGGAAATGTGCAGGAGAGTGTTACACCCAACTACAATGTAACCACCGAAGGCGCAGACACCCTTAAATCGCTCAGGTATCAGGGACTGCACATTGAAA 11) The complementary(Com) sequence(3-5) is-98 nt.: CCCTTTACACGTCCTCTCACAATGTGGGTTGATGTTACATTGGTGGCTTCCGCGTCTGTGGGAATTTAGCGAGTCCATAGTCCCTGACGTGTAACTTT 12) The reverse(Rev) sequence(3-5) is-98 nt.: AAAGTTACACGTCAGGGACTATGGACTCGCTAAATTCCCACAGACGCGGAAGCCACCAATGTAACATCAACCCACATTGTGAGAGGACGTGTAAAGGG 13) The RevCom sequence(5-3) is-98 nt.: TTTCAATGTGCAGTCCCTGATACCTGAGCGATTTAAGGGTGTCTGCGCCTTCGGTGGTTACATTGTAGTTGGGTGTAACACTCTCCTGCACATTTCCC 14) The DNA sequence(5-3) to order with a 10nt overlapping region-59 nt.: GGGAAATGTGCAGGAGAGTGTTACACCCAACTACAATGTAACCACCGAAGGCGCAGACA 15) The RevCom sequence(5-3) to order a 10nt overlapping region-59 nt.: TTTCAATGTGCAGTCCCTGATACCTGAGCGATTTAAGGGTGTCTGCGCCTTCGGTGGTT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Neisseria meningitidis , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Neisseria meningitidis , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -21.70 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -23.01 kcal/mol. The frequency of the MFE structure in the ensemble is 11.96 %. The ensemble diversity is 22.90. The centroid secondary structure in dot-bracket notation with a minimum free energy of -12.92 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Neisseria meningitidis , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Neisseria meningitidis , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

SA631851

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RiboSwitch type

Glycine type switch

Bacteria strain target

Staphylococcus aureus

Length of Switch in nucleotides

Sequence

CGTCACAAAGTTATCCTTTTGCCTGAGAGATTCACTCAAATCTGGCTTGCTCCTTCGGCGATGAATATATCATTCATTCTCTCTAACTTTGATCAT

Above is displayed the nucleotide sequence of the Staphylococcus aureus , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 23 nt. 2) Cytosine(C) in the sequence= 24 nt. 3) Guanine(G) in the sequence= 14 nt. 4) Thiamine(T) in the sequence= 35 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 96 nt. 8) CG percentage of the sequence= 39.58% 9) *Melting temperature of the DNA based on the Wallace formula= 74.12oC 10) The entered DNA sequence(5-3) is-96 nt.: CGTCACAAAGTTATCCTTTTGCCTGAGAGATTCACTCAAATCTGGCTTGCTCCTTCGGCGATGAATATATCATTCATTCTCTCTAACTTTGATCAT 11) The complementary(Com) sequence(3-5) is-96 nt.: GCAGTGTTTCAATAGGAAAACGGACTCTCTAAGTGAGTTTAGACCGAACGAGGAAGCCGCTACTTATATAGTAAGTAAGAGAGATTGAAACTAGTA 12) The reverse(Rev) sequence(3-5) is-96 nt.: TACTAGTTTCAATCTCTCTTACTTACTATATAAGTAGCGGCTTCCTCGTTCGGTCTAAACTCACTTAGAGAGTCCGTTTTCCTATTGAAACACTGC 13) The RevCom sequence(5-3) is-96 nt.: ATGATCAAAGTTAGAGAGAATGAATGATATATTCATCGCCGAAGGAGCAAGCCAGATTTGAGTGAATCTCTCAGGCAAAAGGATAACTTTGTGACG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-58 nt.: CGTCACAAAGTTATCCTTTTGCCTGAGAGATTCACTCAAATCTGGCTTGCTCCTTCGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-58 nt.: ATGATCAAAGTTAGAGAGAATGAATGATATATTCATCGCCGAAGGAGCAAGCCAGATT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus aureus , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus aureus , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -17.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -18.64 kcal/mol. The frequency of the MFE structure in the ensemble is 9.70 %. The ensemble diversity is 16.97. The centroid secondary structure in dot-bracket notation with a minimum free energy of -12.70 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus aureus , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus aureus , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

SE661230

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RiboSwitch type

Glycine type switch

Bacteria strain target

Staphylococcus epidermidis

Length of Switch in nucleotides

143

Sequence

CGTTACAGTATTATCCTTTTGCCTGAGAGTTTCGTTATTTCACTTGCACCTTCGGCGATAGAGAGTCAAAATTGTAATAGACTAAAAACGTTTAACTTATAATGATTCAAGTTTTGATCT CTATTCTCTCTAATACTGATCAA

Above is displayed the nucleotide sequence of the Staphylococcus epidermidis , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 42 nt. 2) Cytosine(C) in the sequence= 26 nt. 3) Guanine(G) in the sequence= 21 nt. 4) Thiamine(T) in the sequence= 54 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 143 nt. 8) CG percentage of the sequence= 32.87% 9) *Melting temperature of the DNA based on the Wallace formula= 73.67oC 10) The entered DNA sequence(5-3) is-143 nt.: CGTTACAGTATTATCCTTTTGCCTGAGAGTTTCGTTATTTCACTTGCACCTTCGGCGATAGAGAGTCAAAATTGTAATAGACTAAAAACGTTTAACTTATAATGATTCAAGTTTTGATCTCTATTCTCTCTAATACTGATCAA 11) The complementary(Com) sequence(3-5) is-143 nt.: GCAATGTCATAATAGGAAAACGGACTCTCAAAGCAATAAAGTGAACGTGGAAGCCGCTATCTCTCAGTTTTAACATTATCTGATTTTTGCAAATTGAATATTACTAAGTTCAAAACTAGAGATAAGAGAGATTATGACTAGTT 12) The reverse(Rev) sequence(3-5) is-143 nt.: AACTAGTCATAATCTCTCTTATCTCTAGTTTTGAACTTAGTAATATTCAATTTGCAAAAATCAGATAATGTTAAAACTGAGAGATAGCGGCTTCCACGTTCACTTTATTGCTTTGAGAGTCCGTTTTCCTATTATGACATTGC 13) The RevCom sequence(5-3) is-143 nt.: TTGATCAGTATTAGAGAGAATAGAGATCAAAACTTGAATCATTATAAGTTAAACGTTTTTAGTCTATTACAATTTTGACTCTCTATCGCCGAAGGTGCAAGTGAAATAACGAAACTCTCAGGCAAAAGGATAATACTGTAACG 14) The DNA sequence(5-3) to order with a 10nt overlapping region-82 nt.: CGTTACAGTATTATCCTTTTGCCTGAGAGTTTCGTTATTTCACTTGCACCTTCGGCGATAGAGAGTCAAAATTGTAATAGAC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-82 nt.: TTGATCAGTATTAGAGAGAATAGAGATCAAAACTTGAATCATTATAAGTTAAACGTTTTTAGTCTATTACAATTTTGACTCT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Staphylococcus epidermidis , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Staphylococcus epidermidis , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -25.90 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -28.88 kcal/mol. The frequency of the MFE structure in the ensemble is 0.80 %. The ensemble diversity is 22.24. The centroid secondary structure in dot-bracket notation with a minimum free energy of -24.20 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Staphylococcus epidermidis , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Staphylococcus epidermidis , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

SA088796

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RiboSwitch type

Glycine type switch

Bacteria strain target

Streptococcus agalactiae

Length of Switch in nucleotides

133

Sequence

AGACGGACTTCTGGAGAGACCTATAAGTAGCAACATCTTTGTATTGACACCAAGATGTGCTCTAGGCGCCGAAGGGGCAAGAAGAGTAAAACAACTCCTCCAATCTCTCAGGCAAAAGGA CAGAAGCTAAAAG

Above is displayed the nucleotide sequence of the Streptococcus agalactiae , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 48 nt. 2) Cytosine(C) in the sequence= 29 nt. 3) Guanine(G) in the sequence= 32 nt. 4) Thiamine(T) in the sequence= 24 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 133 nt. 8) CG percentage of the sequence= 45.86% 9) *Melting temperature of the DNA based on the Wallace formula= 78.65oC 10) The entered DNA sequence(5-3) is-133 nt.: AGACGGACTTCTGGAGAGACCTATAAGTAGCAACATCTTTGTATTGACACCAAGATGTGCTCTAGGCGCCGAAGGGGCAAGAAGAGTAAAACAACTCCTCCAATCTCTCAGGCAAAAGGACAGAAGCTAAAAG 11) The complementary(Com) sequence(3-5) is-133 nt.: TCTGCCTGAAGACCTCTCTGGATATTCATCGTTGTAGAAACATAACTGTGGTTCTACACGAGATCCGCGGCTTCCCCGTTCTTCTCATTTTGTTGAGGAGGTTAGAGAGTCCGTTTTCCTGTCTTCGATTTTC 12) The reverse(Rev) sequence(3-5) is-133 nt.: GAAAATCGAAGACAGGAAAACGGACTCTCTAACCTCCTCAACAAAATGAGAAGAACGGGGAAGCCGCGGATCTCGTGTAGAACCACAGTTATGTTTCTACAACGATGAATATCCAGAGAGGTCTTCAGGCAGA 13) The RevCom sequence(5-3) is-133 nt.: CTTTTAGCTTCTGTCCTTTTGCCTGAGAGATTGGAGGAGTTGTTTTACTCTTCTTGCCCCTTCGGCGCCTAGAGCACATCTTGGTGTCAATACAAAGATGTTGCTACTTATAGGTCTCTCCAGAAGTCCGTCT 14) The DNA sequence(5-3) to order with a 10nt overlapping region-77 nt.: AGACGGACTTCTGGAGAGACCTATAAGTAGCAACATCTTTGTATTGACACCAAGATGTGCTCTAGGCGCCGAAGGGG 15) The RevCom sequence(5-3) to order a 10nt overlapping region-77 nt.: CTTTTAGCTTCTGTCCTTTTGCCTGAGAGATTGGAGGAGTTGTTTTACTCTTCTTGCCCCTTCGGCGCCTAGAGCAC

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Streptococcus agalactiae , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Streptococcus agalactiae , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -35.20 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -37.23 kcal/mol. The frequency of the MFE structure in the ensemble is 3.72 %. The ensemble diversity is 15.18. The centroid secondary structure in dot-bracket notation with a minimum free energy of -32.40 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Streptococcus agalactiae , Glycine type switch.

2D_Structure (A) (B)

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

RiboSwitch_ID:

VC190822

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RiboSwitch type

Glycine type switch

Bacteria strain target

Vibrio cholerae

Length of Switch in nucleotides

100

Sequence

TTTCACTCCTCTGTCCTTTTGCCTGAGAGTTTCACTCTGCATATGCGCAGAGCTTGCTCCTTCGGCGACCGATTAAACGGTTCTCTCCAGAGGTTCCTCC

Above is displayed the nucleotide sequence of the Vibrio cholerae , Glycine type switch.

Sequence information and analysis

1) Adenine(A) in the sequence= 15 nt. 2) Cytosine(C) in the sequence= 32 nt. 3) Guanine(G) in the sequence= 20 nt. 4) Thiamine(T) in the sequence= 33 nt. 5) *Mistaken symbols in the sequence (different from A, a, G, g, T, t, C, c)= 0 6) Position(s) of the wrong symbol(s) found in the sequence= 7) All nucleotides in the sequence= 100 nt. 8) CG percentage of the sequence= 52.00% 9) *Melting temperature of the DNA based on the Wallace formula= 79.50oC 10) The entered DNA sequence(5-3) is-100 nt.: TTTCACTCCTCTGTCCTTTTGCCTGAGAGTTTCACTCTGCATATGCGCAGAGCTTGCTCCTTCGGCGACCGATTAAACGGTTCTCTCCAGAGGTTCCTCC 11) The complementary(Com) sequence(3-5) is-100 nt.: AAAGTGAGGAGACAGGAAAACGGACTCTCAAAGTGAGACGTATACGCGTCTCGAACGAGGAAGCCGCTGGCTAATTTGCCAAGAGAGGTCTCCAAGGAGG 12) The reverse(Rev) sequence(3-5) is-100 nt.: CCTCCTTGGAGACCTCTCTTGGCAAATTAGCCAGCGGCTTCCTCGTTCGAGACGCGTATACGTCTCACTTTGAGAGTCCGTTTTCCTGTCTCCTCACTTT 13) The RevCom sequence(5-3) is-100 nt.: GGAGGAACCTCTGGAGAGAACCGTTTAATCGGTCGCCGAAGGAGCAAGCTCTGCGCATATGCAGAGTGAAACTCTCAGGCAAAAGGACAGAGGAGTGAAA 14) The DNA sequence(5-3) to order with a 10nt overlapping region-60 nt.: TTTCACTCCTCTGTCCTTTTGCCTGAGAGTTTCACTCTGCATATGCGCAGAGCTTGCTCC 15) The RevCom sequence(5-3) to order a 10nt overlapping region-60 nt.: GGAGGAACCTCTGGAGAGAACCGTTTAATCGGTCGCCGAAGGAGCAAGCTCTGCGCATAT

Information about the nucleotide content, melting temperature, and sequence analyses are displayed about the Vibrio cholerae , Glycine type switch.

Mountain plot representation of the switch structure

The plot represents the thermodynamic ensemble of the RNA structure of the Vibrio cholerae , Glycine type switch. In the plot the blue line indicates the predicted centroid structure of the switch. The red line represents the MFE predicted structure and the green line the thermodynamic ensemble of RNA structures. At the lower graph (the black curve), the positional entropy of each position on the switch sequence is displayed.

Free_Energy properties of the riboswitch

The optimal secondary structure in dot-bracket notation with a minimum free energy of -31.10 kcal/mol is given below at structure (A). Results for thermodynamic ensemble prediction The free energy of the thermodynamic ensemble is -32.16 kcal/mol. The frequency of the MFE structure in the ensemble is 17.81 %. The ensemble diversity is 4.20. The centroid secondary structure in dot-bracket notation with a minimum free energy of -31.10 kcal/mol is given below at structure (B).

Information about the free energy of the riboswitch secondary structure based on the MFE and centroid thermodynamic properties of the Vibrio cholerae , Glycine type switch.

2D_Structure (A) (B)

Display of the (A) MFE and (B) centroid secondary structures based on the thermodynamic properties presented above at the "Free_Energy" section of the Vibrio cholerae , Glycine type switch.

Multiple alignment of the Glycine type switches

Coloring of the sequences generated with the ESPript3.x **

Motif_Search

The Pathway which the Glycine type switches involved in.

Multi_resistance strains for the Glycine type switches

*Wallace formula: Tm = 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC).
Wallace RB et al. (1979) Nucleic Acids Res 6:3543-3557, PMID 158748.

**Xavier Robert, Patrice Gouet (2014) Nucleic Acids Research, 42,W1, PMID 24753421

Robert Penchovsky's Website

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Mountain plot representation of the switch structure

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Multiple alignment of the FMN type switches

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Multi_resistance strains for the FMN type switches

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Mountain plot representation of the switch structure

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Multi_resistance strains for the FMN type switches

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Mountain plot representation of the switch structure

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Multi_resistance strains for the FMN type switches

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Mountain plot representation of the switch structure

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The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

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Mountain plot representation of the switch structure

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Multiple alignment of the FMN type switches

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The Pathway which the FMN type switches involved in.

Multi_resistance strains for the FMN type switches

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Mountain plot representation of the switch structure

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Multiple alignment of the FMN type switches