Table 3

The top scored point mutation profiles, only for essential mutations

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


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).

Wozniak et al. BMC Genomics 2012 13(Suppl 7):S23   doi:10.1186/1471-2164-13-S7-S23

Open Data