ICEberg
I. Information of ICE
ICEberg ID288
Name SPI-7 This ICE is derived from experimental literature
FamilySPI-7
OrganismSalmonella enterica subsp. enterica serovar Typhi str. CT18
Size (bp)133500
GC content [Genome] (%)49.68[52.09]
Insertion sitetRNA-PheU
FunctionPathogenicity
Species that ICE can be transferred to-
Nucleotide SequenceAL513382 (complete ICE sequence in this genome)
Replicon chromosome (4809037 bp, BioProject:236) [NC_003198]
Genome coordinates4409574..4543073 
Putative oriT region -
Putative relaxase coordinates: 4527028..4528617; Gene: STY4665;  Family:  MOBH


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 
1STY45134404849..4405046 [-], 198hypothetical protein
2STY45144405069..4405356 [-], 288putative GerE family regulatory protein
3STY45154405353..4406228 [-], 876araC family regulatory protein
4STY45164406494..4406712 [-], 219hypothetical protein
5STY45174407033..4407326 [+], 294conserved hypothetical protein
6STY45184407323..4407814 [+], 492Putative acetyltransferase
7phoN4408055..4408807 [-], 753nonspecific acid phosphatase precursor
8STY45214409652..4410686 [+], 1035hypothetical protein
9STY45224410683..4412047 [+], 1365DNA helicase
10STY45234412040..4413839 [+], 1800hypothetical protein
11STY45244414008..4414313 [+], 306hypothetical protein
12STY45254414441..4415022 [+], 582hypothetical protein
13STY45264415107..4415664 [+], 558hypothetical protein
14STY45284415909..4417252 [+], 1344hypothetical protein
15STY45294417838..4418617 [+], 780hypothetical protein
16topB4418728..4420722 [+], 1995topoisomerase B
17STY45344421390..4421839 [+], 450hypothetical protein
18STY45354421920..4422138 [+], 219hypothetical protein
19ssB4422151..4422687 [+], 537single strand binding protein
20STY45374422753..4423703 [+], 951conserved hypothetical protein (pseudogene)
21pilL4423868..4425112 [+], 1245putative exported proteinTfc2, T4SS component 
22pilM4425115..4425534 [+], 420putative exported protein
23pilN'4425480..4425905 [-], 426PilN lipoprotein homolog (pseudogene)
24pilN'4425981..4427244 [+], 1264pilus assembly protein (pseudogene)
25pilO4427237..4428532 [+], 1296putative pilus assembly protein
26pilP4428630..4429100 [+], 471pilus assembly protein
27pilQ4429110..4430825 [+], 1716nucleotide-binding proteinTraJ_I, T4SS component 
28pilR4430822..4431907 [+], 1086putative membrane protein
29pilS4431907..4432542 [+], 636prepilin
30pilT4432552..4433028 [+], 477putative membrane proteinOrf169_F, T4SS component 
31pilU4433025..4433687 [+], 663prepilin peptidase
32pilV4433684..4434991 [+], 1308prepilin
33'pilV24434993..4435253 [-], 261prepilin, alternative C-terminal region
34rci4435339..4436490 [+], 1152shufflon-specific DNA recombinase
35pilK4436587..4437054 [+], 468putative exported protein
36STY45544437266..4438141 [+], 876hypothetical protein
37STY45574438648..4439562 [+], 915putative membrane protein
38STY45584439581..4440321 [+], 741putative exported proteinTfc3, T4SS component 
39STY45594440435..4440986 [+], 552hypothetical proteinTfc4, T4SS component 
40STY45604441022..4441522 [+], 501hypothetical proteinTfc5, T4SS component 
41STY45614441532..4442101 [+], 570putative membrane protein
42STY45624442121..4444211 [+], 2091hypothetical proteinTfc6, T4SS component 
43STY45634444208..4444966 [+], 759putative membrane proteinTfc8, T4SS component 
44STY45644445185..4445457 [+], 273hypothetical proteinTfc9, T4SS component 
45STY45654445457..4445696 [+], 240putative membrane protein
46STY45664445726..4446088 [+], 363putative membrane proteinTfc10, T4SS component 
47STY45684446469..4447122 [+], 654possible exported proteinTfc12, T4SS component 
48STY45694447122..4448021 [+], 900hypothetical proteinTfc13, T4SS component 
49STY45704448011..4449489 [+], 1479putative exported proteinTfc14, T4SS component 
50STY45714449482..4449925 [+], 444putative lipoproteinTfc15, T4SS component 
51STY45724449922..4450341 [+], 420hypothetical proteinTfc16, T4SS component 
52STY45734450338..4452761 [+], 2424hypothetical proteinTfc16, T4SS component 
53STY45744452916..4453302 [+], 387hypothetical proteinTfc17, T4SS component 
54STY45754453457..4453849 [+], 393hypothetical proteinTfc24, T4SS component 
55STY45764453846..4454814 [+], 969hypothetical proteinTfc23, T4SS component 
56STY45774454829..4456259 [+], 1431hypothetical proteinTfc22, T4SS component 
57STY45784456256..4456588 [+], 333putative membrane protein
58STY45794456592..4458097 [+], 1506putative membrane proteinTfc19, T4SS component 
59STY45804458133..4458522 [-], 390putative membrane protein
60STY45824458746..4459105 [-], 360possible exported protein
61STY45834459393..4460640 [+], 1248conserved hypothetical protein
62STY45844460652..4461266 [+], 615conserved hypothetical protein
63STY45854461477..4462019 [-], 543hypothetical protein
64STY45864463285..4464205 [+], 921hypothetical protein
65STY45874464722..4465231 [+], 510hypothetical protein
66STY45884465327..4465707 [+], 381hypothetical protein
67STY45894466173..4466757 [+], 585hypothetical protein
68STY45904466754..4467050 [+], 297hypothetical protein
69STY45914467128..4467586 [+], 459hypothetical protein
70STY45924467675..4469624 [+], 1950hypothetical protein
71STY45934469696..4470604 [+], 909hypothetical protein
72STY45944470678..4471577 [+], 900hypothetical protein
73STY45954471619..4471978 [+], 360conserved hypothetical protein
74STY45964472078..4472347 [-], 270hypothetical protein
75samB4472479..4473753 [-], 1275UV protection protein
76samA4473753..4507730 [-], 33978UV protection protein (pseudogene)
77STY45994473973..4474350 [+], 378hypothetical protein
78STY46004474437..4474655 [-], 219putative positive regulator of late gene transcription
79STY46014474723..4475823 [-], 1101putative regulator of late gene expression
80STY46024475820..4476305 [-], 486putative phage tail protein
81STY46034476305..4479085 [-], 2781hypothetical protein
82STY46044479078..4479197 [-], 120hypothetical protein
83STY46054479212..4479514 [-], 303putative phage tail protein
84STY46064479569..4480084 [-], 516probable major tail tube protein
85STY46074480094..4481266 [-], 1173probable major tail sheath protein
86'pin4481369..4481590 [-], 222DNA-invertase (pseudogene)
87sopE4481801..4482523 [+], 723invasion-associated secreted protein.VF 
88STY46104482721..4483128 [-], 408putative phage tail fibre protein
89STY46114483135..4484754 [-], 1620probable phage tail fibre protein
90STY46124484751..4485356 [-], 606putative phage tail protein
91STY46134485349..4486257 [-], 909probable phage baseplate assembly protein
92STY46144486244..4486603 [-], 360phage baseplate assembly protein
93STY46154486600..4487178 [-], 579putative phage baseplate assembly protein
94STY46164487247..4487693 [-], 447putative phage tail completion protein
95STY46174487686..4488117 [-], 432putative phage tail protein
96STY46184488213..4488638 [-], 426putative regulatory protein
97STY46194488638..4489015 [-], 378putative membrane protein
98nucD24489020..4489490 [-], 471putative lysozyme
99nucE24489510..4489725 [-], 216possible secretion protein
100STY46224489729..4489932 [-], 204putative phage tail protein
101STY46234489932..4490396 [-], 465putative capsid completion protein
102STY46244490490..4491140 [-], 651putative phage terminase
103STY46254491144..4492208 [-], 1065putative major capsid protein
104STY46264492225..4493058 [-], 834putative capsid protein
105STY46274493201..4494967 [+], 1767probable terminase subunit
106STY46284494964..4496010 [+], 1047probable capsid portal protein
107STY46294496059..4496754 [-], 696hypothetical protein
108STY46304496774..4497838 [-], 1065hypothetical protein
109STY46314497835..4498899 [-], 1065hypothetical protein
110STY46324498909..4499127 [-], 219hypothetical protein
111STY46334499226..4499656 [-], 431SOS operon tum protein (pseudogene)
112STY46354499824..4502238 [-], 2415conserved hypothetical protein
113STY46364502229..4503089 [-], 861DNA adenine methylase
114STY46374503086..4503670 [-], 585putative exonuclease
115STY46384503667..4503894 [-], 228hypothetical protein
116STY46394503894..4504127 [-], 234hypothetical protein
117STY46404504195..4504536 [-], 342conserved hypothetical protein
118STY46414504500..4504700 [-], 201hypothetical protein
119cII4504708..4505217 [-], 510phage regulatory protein
120apl4505250..4505492 [-], 243phage regulatory protein
121cI4505609..4506241 [+], 633phage repressor protein cI
122STY46454506245..4507270 [+], 1026phage integraseIntegrase 
123STY46474507998..4508111 [+], 114hypothetical protein
124STY46484508347..4508634 [+], 288hypothetical protein
125STY46494508645..4509535 [+], 891Putative methyltransferase
126yjhP4509535..4510281 [+], 747conserved hypothetical protein
127vexE4510583..4512553 [-], 1971Vi polysaccharide export proteinVF 
128vexD4512573..4513877 [-], 1305Vi polysaccharide export inner-membrane proteinVF 
129vexC4513900..4514595 [-], 696Vi polysaccharide export ATP-binding proteinVF 
130vexB4514621..4515415 [-], 795Vi polysaccharide export inner-membrane protein (ABC-2 type transporter)VF 
131vexA4515425..4516492 [-], 1068Vi polysaccharide export proteinVF 
132tviE4516537..4518273 [-], 1737Vi polysaccharide biosynthesis protein TviE, Glycosyl transferases group 1VF 
133insB4518289..4518792 [-], 504insertion element IS1 protein InsB
134insA4518711..4518986 [-], 276insertion element IS1 protein
135tviD4519050..4521545 [-], 2496Vi polysaccharide biosynthesis proteinVF 
136tviC4521569..4522615 [-], 1047Vi polysaccharide biosynthesis protein, epimeraseVF 
137tviB4522618..4523895 [-], 1278Vi polysaccharide biosynthesis protein, UDP-glucose/GDP-mannose dehydrogenaseVF 
138tviA4524140..4524679 [-], 540Vi polysaccharide biosynthesis protein
139STY46634525220..4525408 [+], 189hypothetical protein
140STY46644525533..4527044 [+], 1512putative DNA helicaseTraI_F, T4SS component 
141STY46654527028..4528617 [+], 1590hypothetical proteinRelaxase, MOBH Family
142STY46664528781..4529794 [+], 1014probable phage integrase
143STY46674530221..4530514 [+], 294hypothetical protein
144STY46684530511..4530999 [+], 489conserved hypothetical protein
145STY46694531179..4531631 [-], 453putative membrane protein
146STY46704532268..4534553 [-], 2286hypothetical protein
147STY46714534634..4536307 [-], 1674putative membrane protein
148STY46724536854..4537315 [+], 462hypothetical protein
149cII4537312..4537533 [+], 222transcriptional regulatory protein
150STY46744537567..4537710 [-], 144hypothetical protein
151STY46754537926..4538252 [-], 327hypothetical protein
152STY46764538390..4539172 [+], 783hypothetical protein
153STY46774539197..4539409 [-], 213putative membrane protein
154int4539799..4540077 [-], 279integrase (fragment)
155STY46794540153..4541343 [-], 1191putative membrane protein
156int4541654..4542913 [-], 1260bacteriophage integrase
157STY46814543264..4543839 [-], 576putative transcriptional regulator
158dsbD4543876..4545579 [-], 1704thiol:disulfide interchange protein DsbD
159cutA4545555..4545902 [-], 348periplasmic divalent cation tolerance protein CutA
160dcuA4546023..4547324 [-], 1302anaerobic C4-dicarboxylate transporter
 
flank Flanking regions
integrase Gene may contribute to site-specific recombination
conjugation Gene may play role in conjugative transfer
virulence  Gene may be involved in adaptative function

ElementNo. of sequencesDownload
Nucleotide sequences1Fasta
Proteins144Fasta
(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. [PudMed:22247511] in_silico
(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. [PudMed:21402763] experimental
(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. [PudMed:21073066] experimental
(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. [PudMed:20490498] experimental
(5) Seth-Smith HM (2008). SPI-7: Salmonella's Vi-encoding Pathogenicity Island. J Infect Dev Ctries. 2(4):267-71. [PudMed: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. [PudMed:18390666] experimental
(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. [PudMed:16145086] experimental
(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. [PudMed:16041043] experimental
(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. [PudMed:12923078] experimental
(10) Hansen-Wester I; Hensel M (2002). Genome-based identification of chromosomal regions specific for Salmonella spp. Infect Immun. 70(5):2351-60. [PudMed:11953370] in_silico
(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. [PudMed:11677608]
 
experimental experimental literature
in_silico in silico analysis literature