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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).