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Table 3 The top scored point mutation profiles, only for essential mutations

From: An approach to identifying drug resistance associated mutations in bacterial strains

Gene identifier

desc.

NS

NWS

OR

p-value

Gene functional annotation

Penicillin (NWS-threshold: 0.4)

SAR0023(sasH)

G723D

0.55

0.63

8.51

1.87e-05

virulence-associated cell-wall-anchored protein; 5'-nucleotidase

SAR0023(sasH)

T725A

0.54

0.62

8.11

2.23e-05

virulence-associated cell-wall-anchored protein; 5'-nucleotidase

SAR0304

V295I

0.39

0.49

4.48

3.25e-04

acid phosphatase

SAR2791

V182M

0.46

0.46

6.05

5.41e-04

transcriptional regulator, Xre family

SAR2700

N493KD

0.52

0.45

7.72

6.16e-04

ABC transporter permease protein

SAR0233(hmp)

Q333K

0.44

0.44

5.48

7.21e-04

avohemoprotein (nitric oxide dioxygenase)

SAR0318(sbnA)

N25HK

0.44

0.43

5.48

8.36e-04

alpha/beta family hydrolase

SAR2664

V282AT

0.44

0.43

5.48

8.36e-04

probable monooxygenase

SAR2779

S48G

0.44

0.43

5.48

8.36e-04

n-hydroxyarylamine o-acetyltransferase

SAR0318(sbnA)

T138IM

0.43

0.43

5.21

8.36e-04

alpha/beta family hydrolase

SAR0318(sbnA)

T139AQ

0.43

0.43

5.21

8.36e-04

alpha/beta family hydrolase

SAR0023(sasH)

A749TG

0.41

0.43

4.96

8.44e-04

virulence-associated cell-wall-anchored protein; 5'-nucleotidase

SAR0318(sbnA)

R130CG

0.41

0.43

4.96

8.72e-04

alpha/beta family hydrolase

SAR0322(folC)

H201YQE

0.41

0.43

4.96

8.72e-04

macro domain, possibly adp-ribose binding module

SAR0233(hmp)

K323ET

0.40

0.42

4.71

9.08e-04

avohemoprotein (hemoglobin-like protein)

SAR2750(icaC)

I21V

0.40

0.42

4.71

9.46e-04

polysaccharide intercellular adhesin (PIA) biosynthesis protein

SAR0233(hmp)

S309RN

0.39

0.42

4.48

9.46e-04

avohemoprotein (hemoglobin-like protein)

Methicillin (NWS-threshold: 0.25)

SAR0198(oppF)

T287IK

0.10

0.29

2.11

1.41e-04

putative glutathione transporter, ATP-binding component

SAR0420

I72F

0.10

0.29

2.11

1.41e-04

membrane protein

SAR2508(sbi)

S219AT

0.10

0.29

2.11

1.41e-04

IgG-binding protein Sbi

SAR2508(sbi)

N222QK

0.10

0.29

2.11

1.41e-04

IgG-binding protein Sbi

SAR2508(sbi)

K224SDN

0.10

0.29

2.11

1.41e-04

IgG-binding protein Sbi

Tetracycline (NWS-threshold: 0.2)

SAR1840

D291YS

0.18

0.23

5.22

7.09e-04

NAD(FAD)-utilizing dehydrogenases

SAR2336(rpsJ)

K57M

0.29

0.23

9.60

7.32e-04

SSU ribosomal protein S10P (S20E)

SAR0550(rpsL)

K113R

0.36

0.20

13.33

1.14e-03

SSU ribosomal protein S12P (S23E)

Erythromycin (NWS-threshold: 0.2)

SAR0576

A68EV

0.07

0.21

1.54

8.89e-04

phosphoglycolate phosphatase

Gentamicin (NWS-threshold: 0.21)

SAR1840

L289IW

0.33

0.29

15.00

1.43e-03

NAD(FAD)-utilizing dehydrogenases

SAR1840

D291YS

0.33

0.29

15.00

1.43e-03

NAD(FAD)-utilizing dehydrogenases

SAR1840

H327RF

0.33

0.29

15.00

1.43e-03

NAD(FAD)-utilizing dehydrogenases

SAR1167(ylmH)

K215N

0.25

0.29

10.00

1.43e-03

RNA-binding S4 domain-containing protein

SAR1167(ylmH)

R216V

0.25

0.29

10.00

1.43e-03

RNA-binding S4 domain-containing protein

SAR1167(ylmH)

V217L

0.25

0.29

10.00

1.43e-03

RNA-binding S4 domain-containing protein

SAR0547(rpoB)

D471YG

0.17

0.21

6.00

4.61e-03

DNA-directed RNA polymerase beta subunit

SAR1833(trmB)

T54IK

0.17

0.21

6.00

4.61e-03

tRNA (guanine46-n7-)-methyltransferase

Ciprooxacin (NWS-threshold: 0.12)

SAR1367(grlA)

S80YF

1.00

1.00

2244.00

6.03e-30

topoisomerase IV subunit a

SAR0006(gyrA)

S90AL

0.94

0.88

1056.00

1.92e-18

DNA gyrase subunit a

SAR2449(lytT)

V45I

0.21

0.20

17.11

2.06e-04

transcriptional regulator

SAR1840

L289IW

0.12

0.20

8.80

4.56e-04

NAD(FAD)-utilizing dehydrogenases

SAR1793(thiI)

A92ET

0.09

0.20

6.39

2.06e-04

thiamine biosynthesis protein thiI

SAR2212(murA2)

A102T

0.06

0.20

4.12

2.06e-04

UDP-n-acetylglucosamine 1-carboxyvinyltransferase

SAR1367(grlA)

E84KG

0.26

0.15

23.76

9.40e-04

topoisomerase IV subunit a

SAR0235(pstG 1)

F401LV

0.09

0.13

6.39

2.21e-03

PTS system, maltose and glucose-specific IIC component

SAR0400(nfrA)

R194H

0.09

0.13

6.39

2.21e-03

nitroreductase family protein

  1. Summarizing information for the top scored point mutation profiles, only for essential mutations. The conflict mutatations were removed from the table for: tetracycline, erythromycin and gentamicin (for the rest of drugs there were no conflict mutations above the set thresholds). The consequent columns refer to: gene identifier of the corresponding gene family; corresponding position in the multiple alignment and changed amino acids; normalized support (NS); normalized weighted support (NWS); odds ratio (OR); p-value and the gene functional annotation. Thresholds for weighted support are provided in brackets for each drug. Colored gene gain/loss profiles are provided in the supplementary the (additional file 4). Complete results for all the drugs are provided in the supplementary Excel table (additional files 5).
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BMC Genomics

ISSN: 1471-2164

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