ICEberg

ICE
Gene list
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References

I. Information of ICE

ICEberg ID	288
Name	SPI-7
ICEO ID	ICEO_0000120
Organism	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Size (bp)	133500
GC content [Genome] (%)	49.68[52.09]
Insertion site	tRNA-PheU
Function	Pathogenicity
Species that ICE can be transferred to	-
Nucleotide Sequence	AL513382 (complete ICE sequence in this genome)
Replicon	chromosome (4809037 bp, BioProject:236) [NC_003198]
Genome coordinates	4409574..4543073
Putative oriT region	-
Putative relaxase	coordinates: 4527028..4528617; Gene: STY4665; Family: MOB_H

II. ICE interaction with IME/CIME/

The interaction information of SPI-7 is not available.

The graph information of SPI-7 components from AL513382

Complete gene list of SPI-7 from AL513382
#	Gene	Coordinates [+/-], size (bp)	Product (GenBank annotation)	*Reannotation
1	STY4513	4404849..4405046 [-], 198	hypothetical protein
2	STY4514	4405069..4405356 [-], 288	putative GerE family regulatory protein
3	STY4515	4405353..4406228 [-], 876	araC family regulatory protein
4	STY4516	4406494..4406712 [-], 219	hypothetical protein
5	STY4517	4407033..4407326 [+], 294	conserved hypothetical protein
6	STY4518	4407323..4407814 [+], 492	Putative acetyltransferase
7	phoN	4408055..4408807 [-], 753	nonspecific acid phosphatase precursor
8	STY4521	4409652..4410686 [+], 1035	hypothetical protein
9	STY4522	4410683..4412047 [+], 1365	DNA helicase
10	STY4523	4412040..4413839 [+], 1800	hypothetical protein
11	STY4524	4414008..4414313 [+], 306	hypothetical protein
12	STY4525	4414441..4415022 [+], 582	hypothetical protein
13	STY4526	4415107..4415664 [+], 558	hypothetical protein
14	STY4528	4415909..4417252 [+], 1344	hypothetical protein
15	STY4529	4417838..4418617 [+], 780	hypothetical protein
16	topB	4418728..4420722 [+], 1995	topoisomerase B
17	STY4534	4421390..4421839 [+], 450	hypothetical protein
18	STY4535	4421920..4422138 [+], 219	hypothetical protein
19	ssB	4422151..4422687 [+], 537	single strand binding protein
20	STY4537	4422753..4423703 [+], 951	conserved hypothetical protein (pseudogene)
21	pilL	4423868..4425112 [+], 1245	putative exported protein	Tfc2, T4SS component
22	pilM	4425115..4425534 [+], 420	putative exported protein
23	pilN'	4425480..4425905 [-], 426	PilN lipoprotein homolog (pseudogene)
24	pilN'	4425981..4427244 [+], 1264	pilus assembly protein (pseudogene)
25	pilO	4427237..4428532 [+], 1296	putative pilus assembly protein
26	pilP	4428630..4429100 [+], 471	pilus assembly protein
27	pilQ	4429110..4430825 [+], 1716	nucleotide-binding protein	TraJ_I, T4SS component
28	pilR	4430822..4431907 [+], 1086	putative membrane protein
29	pilS	4431907..4432542 [+], 636	prepilin
30	pilT	4432552..4433028 [+], 477	putative membrane protein	Orf169_F, T4SS component
31	pilU	4433025..4433687 [+], 663	prepilin peptidase
32	pilV	4433684..4434991 [+], 1308	prepilin
33	'pilV2	4434993..4435253 [-], 261	prepilin, alternative C-terminal region
34	rci	4435339..4436490 [+], 1152	shufflon-specific DNA recombinase
35	pilK	4436587..4437054 [+], 468	putative exported protein
36	STY4554	4437266..4438141 [+], 876	hypothetical protein
37	STY4557	4438648..4439562 [+], 915	putative membrane protein
38	STY4558	4439581..4440321 [+], 741	putative exported protein	Tfc3, T4SS component
39	STY4559	4440435..4440986 [+], 552	hypothetical protein	Tfc4, T4SS component
40	STY4560	4441022..4441522 [+], 501	hypothetical protein	Tfc5, T4SS component
41	STY4561	4441532..4442101 [+], 570	putative membrane protein
42	STY4562	4442121..4444211 [+], 2091	hypothetical protein	Tfc6, T4SS component
43	STY4563	4444208..4444966 [+], 759	putative membrane protein	Tfc8, T4SS component
44	STY4564	4445185..4445457 [+], 273	hypothetical protein	Tfc9, T4SS component
45	STY4565	4445457..4445696 [+], 240	putative membrane protein
46	STY4566	4445726..4446088 [+], 363	putative membrane protein	Tfc10, T4SS component
47	STY4568	4446469..4447122 [+], 654	possible exported protein	Tfc12, T4SS component
48	STY4569	4447122..4448021 [+], 900	hypothetical protein	Tfc13, T4SS component
49	STY4570	4448011..4449489 [+], 1479	putative exported protein	Tfc14, T4SS component
50	STY4571	4449482..4449925 [+], 444	putative lipoprotein	Tfc15, T4SS component
51	STY4572	4449922..4450341 [+], 420	hypothetical protein	Tfc16, T4SS component
52	STY4573	4450338..4452761 [+], 2424	hypothetical protein	Tfc16, T4SS component
53	STY4574	4452916..4453302 [+], 387	hypothetical protein	Tfc17, T4SS component
54	STY4575	4453457..4453849 [+], 393	hypothetical protein	Tfc24, T4SS component
55	STY4576	4453846..4454814 [+], 969	hypothetical protein	Tfc23, T4SS component
56	STY4577	4454829..4456259 [+], 1431	hypothetical protein	Tfc22, T4SS component
57	STY4578	4456256..4456588 [+], 333	putative membrane protein
58	STY4579	4456592..4458097 [+], 1506	putative membrane protein	Tfc19, T4SS component
59	STY4580	4458133..4458522 [-], 390	putative membrane protein
60	STY4582	4458746..4459105 [-], 360	possible exported protein
61	STY4583	4459393..4460640 [+], 1248	conserved hypothetical protein
62	STY4584	4460652..4461266 [+], 615	conserved hypothetical protein
63	STY4585	4461477..4462019 [-], 543	hypothetical protein
64	STY4586	4463285..4464205 [+], 921	hypothetical protein
65	STY4587	4464722..4465231 [+], 510	hypothetical protein
66	STY4588	4465327..4465707 [+], 381	hypothetical protein
67	STY4589	4466173..4466757 [+], 585	hypothetical protein
68	STY4590	4466754..4467050 [+], 297	hypothetical protein
69	STY4591	4467128..4467586 [+], 459	hypothetical protein
70	STY4592	4467675..4469624 [+], 1950	hypothetical protein
71	STY4593	4469696..4470604 [+], 909	hypothetical protein
72	STY4594	4470678..4471577 [+], 900	hypothetical protein
73	STY4595	4471619..4471978 [+], 360	conserved hypothetical protein
74	STY4596	4472078..4472347 [-], 270	hypothetical protein
75	samB	4472479..4473753 [-], 1275	UV protection protein
76	samA	4473753..4507730 [-], 33978	UV protection protein (pseudogene)
77	STY4599	4473973..4474350 [+], 378	hypothetical protein
78	STY4600	4474437..4474655 [-], 219	putative positive regulator of late gene transcription
79	STY4601	4474723..4475823 [-], 1101	putative regulator of late gene expression
80	STY4602	4475820..4476305 [-], 486	putative phage tail protein
81	STY4603	4476305..4479085 [-], 2781	hypothetical protein
82	STY4604	4479078..4479197 [-], 120	hypothetical protein
83	STY4605	4479212..4479514 [-], 303	putative phage tail protein
84	STY4606	4479569..4480084 [-], 516	probable major tail tube protein
85	STY4607	4480094..4481266 [-], 1173	probable major tail sheath protein
86	'pin	4481369..4481590 [-], 222	DNA-invertase (pseudogene)
87	sopE	4481801..4482523 [+], 723	invasion-associated secreted protein.	VF
88	STY4610	4482721..4483128 [-], 408	putative phage tail fibre protein
89	STY4611	4483135..4484754 [-], 1620	probable phage tail fibre protein
90	STY4612	4484751..4485356 [-], 606	putative phage tail protein
91	STY4613	4485349..4486257 [-], 909	probable phage baseplate assembly protein
92	STY4614	4486244..4486603 [-], 360	phage baseplate assembly protein
93	STY4615	4486600..4487178 [-], 579	putative phage baseplate assembly protein
94	STY4616	4487247..4487693 [-], 447	putative phage tail completion protein
95	STY4617	4487686..4488117 [-], 432	putative phage tail protein
96	STY4618	4488213..4488638 [-], 426	putative regulatory protein
97	STY4619	4488638..4489015 [-], 378	putative membrane protein
98	nucD2	4489020..4489490 [-], 471	putative lysozyme
99	nucE2	4489510..4489725 [-], 216	possible secretion protein
100	STY4622	4489729..4489932 [-], 204	putative phage tail protein
101	STY4623	4489932..4490396 [-], 465	putative capsid completion protein
102	STY4624	4490490..4491140 [-], 651	putative phage terminase
103	STY4625	4491144..4492208 [-], 1065	putative major capsid protein
104	STY4626	4492225..4493058 [-], 834	putative capsid protein
105	STY4627	4493201..4494967 [+], 1767	probable terminase subunit
106	STY4628	4494964..4496010 [+], 1047	probable capsid portal protein
107	STY4629	4496059..4496754 [-], 696	hypothetical protein
108	STY4630	4496774..4497838 [-], 1065	hypothetical protein
109	STY4631	4497835..4498899 [-], 1065	hypothetical protein
110	STY4632	4498909..4499127 [-], 219	hypothetical protein
111	STY4633	4499226..4499656 [-], 431	SOS operon tum protein (pseudogene)
112	STY4635	4499824..4502238 [-], 2415	conserved hypothetical protein
113	STY4636	4502229..4503089 [-], 861	DNA adenine methylase
114	STY4637	4503086..4503670 [-], 585	putative exonuclease
115	STY4638	4503667..4503894 [-], 228	hypothetical protein
116	STY4639	4503894..4504127 [-], 234	hypothetical protein
117	STY4640	4504195..4504536 [-], 342	conserved hypothetical protein
118	STY4641	4504500..4504700 [-], 201	hypothetical protein
119	cII	4504708..4505217 [-], 510	phage regulatory protein
120	apl	4505250..4505492 [-], 243	phage regulatory protein
121	cI	4505609..4506241 [+], 633	phage repressor protein cI
122	STY4645	4506245..4507270 [+], 1026	phage integrase	Integrase
123	STY4647	4507998..4508111 [+], 114	hypothetical protein
124	STY4648	4508347..4508634 [+], 288	hypothetical protein
125	STY4649	4508645..4509535 [+], 891	Putative methyltransferase
126	yjhP	4509535..4510281 [+], 747	conserved hypothetical protein
127	vexE	4510583..4512553 [-], 1971	Vi polysaccharide export protein	VF
128	vexD	4512573..4513877 [-], 1305	Vi polysaccharide export inner-membrane protein	VF
129	vexC	4513900..4514595 [-], 696	Vi polysaccharide export ATP-binding protein	VF
130	vexB	4514621..4515415 [-], 795	Vi polysaccharide export inner-membrane protein (ABC-2 type transporter)	VF
131	vexA	4515425..4516492 [-], 1068	Vi polysaccharide export protein	VF
132	tviE	4516537..4518273 [-], 1737	Vi polysaccharide biosynthesis protein TviE, Glycosyl transferases group 1	VF
133	insB	4518289..4518792 [-], 504	insertion element IS1 protein InsB
134	insA	4518711..4518986 [-], 276	insertion element IS1 protein
135	tviD	4519050..4521545 [-], 2496	Vi polysaccharide biosynthesis protein	VF
136	tviC	4521569..4522615 [-], 1047	Vi polysaccharide biosynthesis protein, epimerase	VF
137	tviB	4522618..4523895 [-], 1278	Vi polysaccharide biosynthesis protein, UDP-glucose/GDP-mannose dehydrogenase	VF
138	tviA	4524140..4524679 [-], 540	Vi polysaccharide biosynthesis protein
139	STY4663	4525220..4525408 [+], 189	hypothetical protein
140	STY4664	4525533..4527044 [+], 1512	putative DNA helicase	TraI_F, T4SS component
141	STY4665	4527028..4528617 [+], 1590	hypothetical protein	Relaxase, MOB_H Family
142	STY4666	4528781..4529794 [+], 1014	probable phage integrase
143	STY4667	4530221..4530514 [+], 294	hypothetical protein
144	STY4668	4530511..4530999 [+], 489	conserved hypothetical protein
145	STY4669	4531179..4531631 [-], 453	putative membrane protein
146	STY4670	4532268..4534553 [-], 2286	hypothetical protein
147	STY4671	4534634..4536307 [-], 1674	putative membrane protein
148	STY4672	4536854..4537315 [+], 462	hypothetical protein
149	cII	4537312..4537533 [+], 222	transcriptional regulatory protein
150	STY4674	4537567..4537710 [-], 144	hypothetical protein
151	STY4675	4537926..4538252 [-], 327	hypothetical protein
152	STY4676	4538390..4539172 [+], 783	hypothetical protein
153	STY4677	4539197..4539409 [-], 213	putative membrane protein
154	int	4539799..4540077 [-], 279	integrase (fragment)
155	STY4679	4540153..4541343 [-], 1191	putative membrane protein
156	int	4541654..4542913 [-], 1260	bacteriophage integrase
157	STY4681	4543264..4543839 [-], 576	putative transcriptional regulator
158	dsbD	4543876..4545579 [-], 1704	thiol:disulfide interchange protein DsbD
159	cutA	4545555..4545902 [-], 348	periplasmic divalent cation tolerance protein CutA
160	dcuA	4546023..4547324 [-], 1302	anaerobic C4-dicarboxylate transporter

Flanking regions

Element	No. of sequences	Download
Nucleotide sequences	1	Fasta
Proteins	144	Fasta

(1) Seth-Smith HM; Fookes MC; Okoro CK; Baker S; Harris SR; Scott P; Pickard D; Quail MA; Churcher C; Sanders M; Harmse J; Dougan G; Parkhill J; Thomson NR (2012). Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae. J Bacteriol. 194(6):1494-504. [PubMed:22247511]

(2) Janis C; Grant AJ; McKinley TJ; Morgan FJ; John VF; Houghton J; Kingsley RA; Dougan G; Mastroeni P (2011). In vivo regulation of the Vi antigen in Salmonella and induction of immune responses with an in vivo-inducible promoter. Infect Immun. 79(6):2481-8. [PubMed:21402763]

(3) Maurya P; Gulati AK; Nath G (2010). Status of Vi gene, its expression and Salmonella Pathogenicity Island (SPI-7) in Salmonella Typhi in India. Southeast Asian J Trop Med Public Health. 41(4):913-9. [PubMed:21073066]

(4) Parvathi A; Vijayan J; Murali G; Chandran P (2011). Comparative virulence genotyping and antimicrobial susceptibility profiling of environmental and clinical Salmonella enterica from Cochin, India. Curr Microbiol. 62(1):21-6. [PubMed:20490498]

(5) Seth-Smith HM (2008). SPI-7: Salmonella's Vi-encoding Pathogenicity Island. J Infect Dev Ctries. 2(4):267-71. [PubMed:19741287]

(6) Baker S; Pickard D; Whitehead S; Farrar J; Dougan G (2008). Mobilization of the incQ plasmid R300B with a chromosomal conjugation system in Salmonella enterica serovar typhi. J Bacteriol. 190(11):4084-7. [PubMed:18390666]

(7) Baker S; Sarwar Y; Aziz H; Haque A; Ali A; Dougan G; Wain J; Haque A (2005). Detection of Vi-negative Salmonella enterica serovar typhi in the peripheral blood of patients with typhoid fever in the Faisalabad region of Pakistan. J Clin Microbiol. 43(9):4418-25. [PubMed:16145086]

(8) Faucher SP; Curtiss R 3rd; Daigle F (2005). Selective capture of Salmonella enterica serovar typhi genes expressed in macrophages that are absent from the Salmonella enterica serovar Typhimurium genome. Infect Immun. 73(8):5217-21. [PubMed:16041043]

(9) Pickard D; Wain J; Baker S; Line A; Chohan S; Fookes M; Barron A; Gaora PO; Chabalgoity JA; Thanky N; Scholes C; Thomson N; Quail M; Parkhill J; Dougan G (2003). Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. J Bacteriol. 185(17):5055-65. [PubMed:12923078]

(10) Hansen-Wester I; Hensel M (2002). Genome-based identification of chromosomal regions specific for Salmonella spp. Infect Immun. 70(5):2351-60. [PubMed:11953370]

(11) Parkhill J; Dougan G; James KD; Thomson NR; Pickard D; Wain J; Churcher C; Mungall KL; Bentley SD; Holden MT; Sebaihia M; Baker S; Basham D; Brooks K; Chillingworth T; Connerton P; Cronin A; Davis P; Davies RM; Dowd L; White N; Farrar J; Feltwell T; Hamlin N; Haque A; Hien TT; Holroyd S; Jagels K; Krogh A; Larsen TS; Leather S; Moule S; O'Gaora P; Parry C; Quail M; Rutherford K; Simmonds M; Skelton J; Stevens K; Whitehead S; Barrell BG (2001). Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature. 413(6858):848-52. [PubMed:11677608]

experimental literature

in silico analysis literature