Table 1 Genes of the SOS regulon

VC0082

rmuC

DNA recombination protein rmuC

cp : cell process

2.1.3 : DNA recombination; 5.8 : SOS response ;

8.1 : DNA replication, recombination, and repair ;

19.7

VC0092

lexA

LexA repressor

r : regulator

2.1.4 : DNA repair ; 2.2.2 : Transcription related ; 3.1.2.3 : Repressor ; 3.3.2 : Regulon (a network of operons encoding related functions) ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 9 : Transcription ; 12.1 : DNA interactions ; 15.10 : Adaptations to atypical conditions ;

25.5

VC0190

uvrD

DNA helicase II

e : enzyme

2.1.1 : DNA replication ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ;

9.1

VC0196

recQ

ATP-dependent DNA helicase recQ

e : enzyme

2.1.1 : DNA replication ; 2.1.3 : DNA recombination ; 2.1.4 : DNA repair; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8 : DNA metabolism ;

2.4

VC0394

uvrA

UvrABC system protein A

e : enzyme

2.1.4 : DNA repair ; 5.6.1 : Radiation ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ;

9.9

VC0397

ssb, exrB, lexC

Single-stranded DNA-binding protein

cp : cell process

2.1.3 : DNA recombination ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ;

3.8

VC0543

recA

Protein recA

e : enzyme

2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 2.3.6 : Turnover, degradation ; 3.1.3.4 : Proteases, cleavage of compounds ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 11.4 : Degradation of proteins, peptides, and glycopeptides ; 12.3 : Protein interactions ; 15.10 : Adaptations to atypical conditions ;

16.4

VC0544

recX

Regulatory protein recX

r : regulator

Modulates recA activity; 5.8 : SOS response ;

15.10 : Adaptations to atypical conditions ;

11.4

VC0852

recN, radB

DNA repair protein recN

cp : cell process

2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ;

47.0

VC1191

unfA

putative Superfamily II DNA and RNA helicase

pe : putative enzyme

; 5.8 : SOS response ;

32.7

VC1368

unfB

conserved hypothetical protein

o : ORF of unknown function

; 5.8 : SOS response ;

16.0

VC1453

rstB1

RstB phage-related integrase

e : enzyme

8.1.4 : Integration, recombination ; 5.8 : SOS response ;

17.2 : Prophage functions ;

25.7

VC1454

rstA1

RstA phage-related replication protein

h : extrachromosomal origin

8.1.2 : Replication; 5.8 : SOS response ;;

17.2 : Prophage functions ;

33.8

VC1455

rstR1

Cryptic phage CTXphi transcriptional repressor rstR

r : regulator

3.1.2.3 : Repressor ; 7.1 : Cytoplasm ; 8.1.3 : Regulation ; 5.8 : SOS response ;

12 : Regulatory functions ; 17.2 : Prophage functions ;

0.3

VC1462

rstB2

RstB phage-related integrase

e : enzyme

8.1.4 : Integration, recombination; 5.8 : SOS response ;

17.2 : Prophage functions ;

28.2

VC1463

rstA2

RstA phage-related replication protein

h : extrachromosomal origin

8.1.2 : Replication; 5.8 : SOS response ;

17.2 : Prophage functions ;

33.7

VC1464

rstR2

Cryptic phage CTXphi transcriptional repressor rstR

r : regulator

3.1.2.3 : Repressor ; 7.1 : Cytoplasm ; 8.1.3 : Regulation; 5.8 : SOS response ;

12 : Regulatory functions ; 17.2 : Prophage functions ;

0.3

VC1845

ruvB

Holliday junction ATP-dependent DNA helicase ruvB

e : enzyme

2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ;

4.1

VC1846

ruvA

Holliday junction ATP-dependent DNA helicase ruvA

e : enzyme

2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ;

8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ;

4.7

VC2043

topB

DNA topoisomerase 3

e : enzyme

2.1.1 : DNA replication ; 2.2.2 : Transcription related ; 3.1.1.1 : DNA bending, supercoiling, inversion ; 7.1 : Cytoplasm; 5.8 : SOS response ;

8.1 : DNA replication, recombination, and repair ; 9 : Transcription ; 12 : Regulatory functions ;

4.8

VC2287

dinB

DNA polymerase IV

e : enzyme

2.1.1 : DNA replication; 5.8 : SOS response ;

8.1 : DNA replication, recombination, and repair ;

19.4

VC2326

yebG

dsDNA-binding SOS-regulon protein

pcp : putative cell process

; 5.8 : SOS response ;

4.0

VC2711

recG, spoV, radC

ATP-dependent DNA helicase recG

e : enzyme

2.1.1 : DNA replication; 5.8 : SOS response ;

8 : DNA metabolism ;

4.1

VCA0291

intIA

Site-specific recombinase IntIA

e : enzyme

2.1.3 : DNA recombination ; 7.1 : Cytoplasm ; 8.1.4 : Integration, recombination; 5.8 : SOS response ;

8.1 : DNA replication, recombination, and repair ;

14.4

VCA0952

vpsT, csgD

LuxR family transcriptional regulator VpsT

r : regulator

3 : Regulation ; 3.1.2 : Transcriptional level ; 5.12 : Biofilm production ; 5.8 : SOS response ;

12 : Regulatory functions ; 12.1 : DNA interactions ; 14 : Cell envelope ; 14.1 : Surface structures ; 14.3 : Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides ;

2.8

VC0083

ubiE

Ubiquinone/menaquinone biosynthesis methyltransferase UbiE

e : enzyme

1.5.3.11 : Menaquinone (MK), ubiquinone (Q) ;

4.5 : Menaquinone and ubiquinone ;

9.0

VC0084

ubiJ

Ubiquinone biosynthesis protein UbiJ

e : enzyme

1.5.3.11 : Menaquinone (MK), ubiquinone (Q) ;

4.5 : Menaquinone and ubiquinone ;

5.2

VC0085

ubiB

ubiquinone biosynthesis protein UbiB

e : enzyme

1.5.3.11 : Menaquinone (MK), ubiquinone (Q) ; 5 : Inner membrane protein

4.5 : Menaquinone and ubiquinone ;

3.7

VC0086

tatA

Sec-independent protein translocase TatA

t : transporter

4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family ; 4.S.160 : protein ;

7 : Transport and binding proteins ;

3.2

VC0087

tatB

Sec-independent protein translocase protein TatB

t : transporter

4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family ; 4.S.160 : protein ;

7 : Transport and binding proteins ;

4.0

VC0088

tatC

Sec-independent protein translocase protein TatC

t : transporter

4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family ; 4.S.160 : protein ; 5 : Inner membrane protein

7 : Transport and binding proteins ;

5.5

VC0091

putative O-Methyltransferase involved in polyketide biosynthesis

pe : putative enzyme

5.6.4 : Drug resistance/sensitivity ;

15.8 : Toxin production and resistance ;

13.7

VC0851

smpA

small protein A

lp : lipoprotein

12.7

VC1190

putative phosphoribosylaminoimidazole-succinocarboxamide synthase PurC

pe : putative enzyme

1.5.2.1 : Purine biosynthesis ; 2 : Cytoplasmic

2.3 : Purine ribonucleotide biosynthesis ;

16.8

VC1369

putative ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic component

pt : putative transporter

4.3.A.1.p : periplasmic binding component; 9 : Periplasmic

7 : Transport and binding proteins ;

2.4

VC1370

putative Signal transduction histidine kinase domain, Methyl-accepting chemotaxis domain and GGDEF family protein

pr : putative regulator

3 : Regulation ; 5 : Inner membrane protein

12 : Regulatory functions ;

2.3

VC1461

cep

Colonization factor

f : factor

5.13 : Virulence associated ; 5 : Inner membrane protein

15.9 : Pathogenesis ;

52.4