Genome Information

PAthogenisity Island DataBase (PAI DB)

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Genome Information

• General information

Accession:

Strain :

Salmonella enterica

Type :

Size :

G+C content :

[Note]

• PAIs (PAI reported to be located in this genome)

No	Name	Start	End	Size(bp)	Insertion Site	Function
1	SPI-6	302092	360757	58666	tRNA-asp	safA-D and tcsA-R chaperone-usher fimbrialoperons6
2	SPI-5	1085068	1092563	7496	tRNA-ser	Effector proteins for SPI-1 and SPI-2 (SopB, SigD, PipB)
3	SPI-2	1624920	1666524	41605	tRNA-val	Type III secretion system, required for systemic infection and intracellular pathogenesis by facilitating replication of intracellular bacteria within membrane-bound Salmonella-containing vacuoles
4	SPI-9	2743495	2759190	15696	-	Type I secretory apparatus, large RTX-like protein
5	SPI-1	2858736	2900586	41851	fhlA/mutS	Type III secretion system, invasion into epithelial cells, apoptosis (InvA, OrgA, SptP, SipA, SipB, SipC, SipD, SopE, prgH)
6	SPI-8	3132530	3139414	6885	tRNA-phe	Two bacteriocin pseudogenes, genes conferring immunity to the bacteriocins
7	SPI-3	3883613	3900553	16941	tRNA-pro	Invasion, survival in monocytes, Mg2+ uptake (MgtC, B, MarT, MisL)
8	SPI-4	4322993	4346383	23391	ssb	Type I secretion system, putative toxin secretion, apoptosis, required for intracellular survival in macrophages, genes weakly similar to RTX-like toxins
9	SPI-7	4409511	4543148	133638	tRNA-phe	Vi exopolysaccharide, SopE prophage and a type IVB pilus operon
10	SPI-10	4683605	4716538	32934	tRNA-leu	Phage 46 and the sefA-R chaperone-usher fimbrial operon

• cPAIs (PAI-like region overlapping genomic islands (candidate PAI))

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No	Start	End	Size(bp)	No. of ORFs	G+C content	No. of homologs of PAI-virulence genes	PAIs homologous to this region
1	292653	360757	68105	71	51.44 %	8	tcd island (Photorhabdus luminescens W14) SPI-6 (Salmonella enterica subsp. enterica serovar Typhi CT18)
2	1082125	1106407	24283	27	50.44 %	9	tcd island (Photorhabdus luminescens W14) SPI-5 (Salmonella enterica 2229) SPI-5 (Salmonella typhimurium LT2) SPI-5 (Salmonella enterica subsp. enterica serovar Typhi CT18) SPI-5 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67)
3	1624920	1666524	41605	47	47.36 %	43	LEE (Citrobacter rodentium DBS100) LEE (Escherichia coli E2348/69) LEE (Escherichia coli ATCC43895) LEE (Escherichia coli 71074) LEE (Escherichia coli 83/39) LEE (Escherichia coli RW1374) LEE (Escherichia coli RDEC-1) LEE (Escherichia coli O157:H7 EDL933) LEE (Escherichia coli O157:H7 Sakai) LEE (Escherichia coli 12009) LEE (Escherichia coli 11368) LEE (Escherichia coli 11128) LEE II (Escherichia coli 413/89-1) SPI-2 (Salmonella enterica LT2) SPI-2 (Salmonella enterica SL1344) SPI-2 (Salmonella typhimurium LT2) SPI-2 (Salmonella enterica subsp. enterica serovar Typhi CT18) SPI-2 (Salmonella enterica subsp. enterica serovar Typhi Ty2) SPI-2 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67) SESS LEE (Salmonella enterica S1296) SESS LEE (Salmonella enterica S1635) Not named (Yersinia pestis CO92)
4	1779602	1790852	11251	18	40.65 %	3	SPI-11 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67)
5	2290935	2310613	19679	22	56.48 %	2	Not named (Cronobacter sakazakii ATCC BAA-894) PAGI-2(C) (Pseudomonas aeruginosa C) SPI-12 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67)
6	2858736	2900586	41851	48	45.68 %	37	LIM (Escherichia coli O157:H7 Sakai) TTSS locus (Photorhabdus luminescens W14) SPI-1 (Salmonella typhimurium LT2) SPI-1 (Salmonella enterica subsp. enterica serovar Typhi CT18) SPI-1 (Salmonella enterica subsp. enterica serovar Typhi Ty2) SPI-1 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67) centisome 63 pathogenicity island (Salmonella enterica SL1344) SSR-1 (Sodalis glossinidius ) SSR-2 (Sodalis glossinidius )
7	4321410	4349418	28009	11	44.85 %	8	SPI-4 (Salmonella enterica LT2) SPI-4 (Salmonella enterica ST4/74) SPI-4 (Salmonella typhimurium LT2) SPI-4 (Salmonella enterica subsp. enterica serovar Typhi CT18) SPI-4 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67)
8	4407033	4543148	136116	161	49.66 %	28	ICEPmu1 (Pasteurella multocida 36950) Not named (Proteus mirabilis HI4320) PAPI-1 (Pseudomonas aeruginosa PA14) ExoU island A (Pseudomonas aeruginosa 6077) PAGI-2(C) (Pseudomonas aeruginosa C) PAGI-3(SG) (Pseudomonas aeruginosa SG17M) PAGI-5 (Pseudomonas aeruginosa PSE9) PAGI-6 (Pseudomonas aeruginosa PSE9) PPHGI-1 (Pseudomonas syringae 1302A) SPI-7 (Salmonella enterica Ty2) SPI-7 (Salmonella enterica subsp. enterica serovar Typhi CT18) SPI-7 (Salmonella enterica subsp. enterica serovar Typhi Ty2) YAPI (Yersinia pseudotuberculosis 32777) YAPI (Yersinia enterocolitica 8081) YAPI (Yersinia pseudotuberculosis IP 31758)
9	4683605	4716538	32934	31	46.61 %	4	SPI-10 (Salmonella enterica subsp. enterica serovar Typhi CT18)

• nPAIs (PAI-like region not overlapping genomic islands (non-probable PAI))

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No	Start	End	Size(bp)	No. of ORFs	G+C content	No. of homologs of PAI-virulence genes	PAIs homologous to this region
1	2597945	2615051	17107	5	57.13 %	4	CS54 island (Salmonella enterica ATCC14028)
2	2743495	2778844	35350	20	55.82 %	5	PAI III 536 (Escherichia coli 536) PAGI-6 (Pseudomonas aeruginosa PSE9) SPI-7 (Salmonella enterica subsp. enterica serovar Typhi CT18) SPI-7 (Salmonella enterica subsp. enterica serovar Typhi Ty2) SPI-9 (Salmonella enterica subsp. enterica serovar Typhi CT18)
3	3882205	3900553	18349	16	47.52 %	9	SPI-3 (Salmonella enterica 14028s) SPI-3 (Salmonella typhimurium LT2) SPI-3 (Salmonella enterica subsp. enterica serovar Typhi CT18) SPI-3 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67)

• REIs (REI reported to be located in this genome)

• cREIs (REI-like region overlapping genomic islands (candidate REI))

*

No	Start	End	Size(bp)	No. of ORFs	G+C content	No. of homologs of REI-resistance genes	REIs homologous to this region
1	2045762	2056416	10655	19	51.56 %	1	PAI IV 536 (Escherichia coli 536) PAI IV APEC-O1 (Escherichia coli APEC O1)

• nREIs (REI-like region not overlapping genomic islands (non-probable REI))

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