Table 3 Gene circuits linked to pathogenic phenotype. Gene symbols in the table indicate orthologs in the circuit, which are abundant in pathogenic but rarely found in nonpathogenic strains

1

Two Component system

Mg2+ starvation, antimicrobial peptide

pagC, pagO, pagD, pagK, pgtE

S. enterica*, B. aphidicola, E. coli*, P. ananatis, Y. pseudotuberculosis

2

Two Component system

Hexose phosphate uptake

uhpC, uhpA, uhpT

C. trachomatis, E. coli*, S. enterica*, S. aureus, L. monocytogenes

3

Two Component system

Competence Stimulating Peptide

ABCC-BAC.COMA, comA, comB, comC, comD, comE

S. pneumoniae, L. casei, L. rhamnosus, S. equi, L. plantarum

4

Two Component system

Hypoxia,Oxygen, Nitrogen asssimilation

devS, nreA, nreB, narT

S. aureus*, M. tuberculosis, M. bovis, M. canettii, P. polymyxa

5

Two Component system

Phosphpglycerate transport

pgtC, pgtB, pgtA, pgtP

S. enterica*, C. jejuni, V. cholerae, K. pneumoniae, E. coli

6

Biosynthesis of siderophore group nonribosomal peptides

Yersiniabactin

irp1, HMWP1, irp5, ybtE, irp3, ybtU

E. coli* , Y. pestis, R. solanacearum, C. diphtheriae, K. pneumoniae

7

Biosynthesis of siderophore group nonribosomal peptides

Pyochelin

pchF, pchG, pchD, pchE

P. aeruginosa, B. pseudomallei, B. cenocepacia, A. dieselolei, A. lipoferum

8

Bacterial secretion system

Type III

yscF, yscO, yscP, yscX, yscC, yscW

C. trachomatis*, S. enterica, E. coli*, C. psittaci, P. aeruginosa

9

Bacterial secretion system

Type V

vacA, yadA, yadB_C

H. pylori*, Y. pestis, Y. pseudotuberculosis, Y. enterocolitica, H. cetorum

10

Peptidoglycan biosynthesis

Peptidoglycan branch

sgtA, sgtB, femA, pbpA, femB,

S. aureus, C. Arthromitus, E. sp., S.

11

Carotenoid biosynthesis

Terpenpid backbone to Staphyloxanthin

crtM, crtP, crtQ, K10212, crtO

S. aureus*, B. megaterium, C. sp., S. lugdunensis, B. infantis

12

Salmonella infection

Translocon

sipB, ipaB, bipB, sipC, ipaC, bipC, sipD, ipaD, bipD, sseB, sseC, sseD

S. enterica*, B. pseudomallei, E. coli*, S. baltica, B. mallei

13

Salmonella infection

Type III secretion system/SPI-2 encoded

sseJ, sifA, sseF, sseG, pipB2, sspH2, sseI, srfH, spvB

S. enterica*, S. baltica, E. tarda, Y. enterocolitica, C. violaceum

14

Pentose phosphate pathway

D-Glucosaminate metabolism

dgaA-dgaE, PTS-Dga-EIIA, PTS-Dga-EIID, PTS-Dga-EIIB, PTS-Dga-EIIC

S. enterica*, E. coli*, E. faecalis, C. difficile, L. casei

15

Bacterial invasion of epithelial cells

ECM-receptor interaction

pfbA, sfb1, fnbA, fnbB

S. aureus, S. pyogenes, S. pneumoniae, S. dysgalactiae, S. equi

16

Phosphotransferase system

Sorbose to Sorbose 1-phosphate

PTS-Sor-EIIC, sorA, PTS-Sor-EIID, sorM, PTS-Sor-EIIA, sorF, PTS-Sor-EIIB, sorB

E. coli*, K. pneumoniae, L. casei, L. rhamnosus, S. flexneri

17

Phosphotransferase system

D-Glucosaminate to D-Glucosaminate 6-P

PTS-Dga-EIIC, dgaA-dga-D, PTS-Dga-EIIA, PTS-Dga-EIID,, PTS-Dga-EIIB

S. enterica*, E. coli*, E. faecalis, C. difficile, L. casei

18

Amino nucleotide sugar metabolism

CMP-Pse metabolism

pseC, pseH, pseF, UAP1

C. trachomatis, H. pylori*, C. jejuni, C. psittaci, P. acnes

19

Plant-pathogen interaction

Bacterial secretion system

hopAB, avrPtoB, avrPto1, avrRpm1, avrXccC, avrB

P. syringae, _., X. campestris, _.

20

Bacterial invasion of epithelial cells

Type III - Salmonella

sipA-sipD, ipaA-ipaD, bipD, bipC, bipB, sopD, sptP, sopE, ipgD, sopB

S. enterica, B. pseudomallei, E. coli, B. mallei, B. thailandensis

21

Bacterial invasion of epithelial cells

Type III - Shigella

sipC, ipaA-ipaC, bipC, sipB, bipB, ipgB1, espG, virA, ipgB2, ipgD, sopB

S. enterica, E. coli, B. pseudomallei, B. mallei, B. thailandensis

22

Vibrio cholerae infection

Type II secretion system

ctxA, ctxB, ace, rtxA

V. cholerae*, E. coli*, V. vulnificus, Y. enterocolitica, A. hydrophila

23

Vibrio cholerae infection

Type IV pilus

tcpA, tcpB, tcpC, tcpD, tcpE, tcpF

V. cholerae*, C. rodentium, E. cloacae, R. aquatilis, R. sp.

24

Vibrio cholerae pathogenic cycle

Quorum Sensing

luxQ, luxU, qrr, tcpB, K10917, aphA, tcpH, tcpP

V. cholerae*, V. vulnificus, V. fischeri, V. parahaemolyticus, V. sp.

25

Epithelial cell signaling in Helicobacter pylori infection

Type IV secretion system

cag1, cag2, cag1, cag2, cag3, virB11, lvhB11, cag7-cag25

H. pylori*, R. prowazekii, L. pneumophila, R. rickettsii, S. meliloti

26

Epithelial cell signaling in Helicobacter pylori infection

Adhesins

hopC, alpA, hopB, alpB, hopZ, K15846, hpaA, sdbA, sabA

H. pylori*, L. pneumophila*, H. cetorum, H. acinonychis, H. bizzozeronii

27

Pathogenic Escherichia coli infection

Intimate adhesion/Type III secretion system

espG, virA, tir, espF, map, eae, nleA, nleH, espH, tccP, espG2

E. coli*, S. flexneri, S. sonnei, C. rodentium, S. boydii

28

Shigellosis

Motility

icsA, virG, espG, virA, icsB, bopA

E. coli, B. pseudomallei, B. mallei, S. flexneri, S. sonnei

29

Shigellosis

Type III Secretion/Downsteam

ipgB1-2, ipaH9.8, ospE-G, espO, mkaD, sipA-D, ipaA-D, bipB-D, ipgD, sopB

S. enterica*, E. coli*, B. pseudomallei*, B. mallei*, E. tarda

30

Salmonella infection

Type III secretion system/SPI-1 encoded

sipB, ipaB, bipB, sopE, ipgD, sopB, sipA, ipaA, sptP, yopJ

S. enterica*, Y. pestis, B. pseudomallei, E. coli*, B. mallei*

31

Pertussis

Type IV secretion system

ptxD, ptxB, ptxE, ptxC, ptxA

S. enterica*, B. pertussis, Y. enterocolitica, B. bronchiseptica, B. parapertussis

32

Legionellosis

Adhesion/Cell entry

sdeA, laiA, rtxA1, rtxA, enhC, lpnE

L. pneumophila*, C. burnetii, L. longbeachae,

33

Legionellosis

Dot/Icm secretion system

ralF, lidA, sidC, legK1, lgt1_2_3, sidI,M, FlepB, vipA,D,E, sdbA, sdcA, drrA, lubX

L. pneumophila*, L. longbeachae,

34

Staphylococcus aureus infection

Colonization/MSCRMMs

clfB, isdA, sdrC_D_E, sasG

S. aureus*, C. pseudotuberculosis, S. epidermidis, S. pseudintermedius, E. casseliflavus

35

Staphylococcus aureus infection

Surface proteins

spa, sbi, clfA, sak, scn, scin, fib, efb, chp, chips, flr, flipr

S. aureus*, S. lugdunensis*, S. pseudintermedius, B. thuringiensis, S. carnosus