ICEberg
ICEberg ID288
NameSPI-7
FamilySPI-7
OrganismSalmonella enterica subsp. enterica serovar Typhi str. CT18
Size (bp)133500
GC content [Genome] (%)50 [52]
Insertion sitetRNA-PheU
FunctionPathogenicity
Species that ICE can be transferred to-
Nucleotide SequenceAL513382 (complete ICE sequence in this genome)
Replicon chromosome (4809037 bp, Project:236) [NC_003198]
Genome coordinates4409574..4543073
Link to view genome context of this ICE in the genome browser
experimental This is a ICE derived from experimental literature.
Complete gene list of SPI-7 form AL513382
#GeneCoordinates [+/-], size (bp)Protein GI Product *
1STY45134404849..4405046 [-], 19816505299 hypothetical protein
2STY45144405069..4405356 [-], 28816505300 putative GerE family regulatory protein
3STY45154405353..4406228 [-], 87616505301 araC family regulatory protein
4STY45164406494..4406712 [-], 21916505302 hypothetical protein
5STY45174407033..4407326 [+], 29416505303 conserved hypothetical protein
6STY45184407323..4407814 [+], 49216505304 Putative acetyltransferase
7phoN4408055..4408807 [-], 75316505305 nonspecific acid phosphatase precursor
8STY45214409652..4410686 [+], 103516505306  [UniProt]  [KEGG]hypothetical protein
9STY45224410683..4412047 [+], 136516505307  [UniProt]  [KEGG]DNA helicase
10STY45234412040..4413839 [+], 180016505308  [UniProt]  [KEGG]hypothetical protein
11STY45244414008..4414313 [+], 30616505309  [UniProt]  [KEGG]hypothetical protein
12STY45254414441..4415022 [+], 58216505310  [UniProt]  [KEGG]hypothetical protein
13STY45264415107..4415664 [+], 55816505311  [UniProt]  [KEGG]hypothetical protein
14STY45284415909..4417252 [+], 134416505312  [UniProt]  [KEGG]hypothetical protein
15STY45294417838..4418617 [+], 78016505313  [UniProt]  [KEGG]hypothetical protein
16topB4418728..4420722 [+], 199516505314  [UniProt]  [KEGG]topoisomerase B
17STY45344421390..4421839 [+], 45016505315  [UniProt]  [KEGG]hypothetical protein
18STY45354421920..4422138 [+], 21916505316  [UniProt]  [KEGG]hypothetical protein
19ssB4422151..4422687 [+], 53716505317  [UniProt]  [KEGG]single strand binding proteinVF
20STY45374422753..4423703 [+], 951pseudogene conserved hypothetical protein (pseudogene)
21pilL4423868..4425112 [+], 124516505318  [UniProt]  [KEGG]putative exported proteinVF
22pilM4425115..4425534 [+], 42016505319  [UniProt]  [KEGG]putative exported protein
23pilN'4425480..4425905 [-], 42616505320 PilN lipoprotein homolog (pseudogene)
24pilN'4425981..4427244 [+], 1264pseudogene pilus assembly protein (pseudogene)
25pilO4427237..4428532 [+], 129616505321  [UniProt]  [KEGG]putative pilus assembly protein
26pilP4428630..4429100 [+], 47116505322  [UniProt]  [KEGG]pilus assembly proteinVF
27pilQ4429110..4430825 [+], 171616505323  [UniProt]  [KEGG]nucleotide-binding proteinVF
28pilR4430822..4431907 [+], 108616505324  [UniProt]  [KEGG]putative membrane proteinVF
29pilS4431907..4432542 [+], 63616505325  [UniProt]  [PDB]  [KEGG]prepilinVF
30pilT4432552..4433028 [+], 47716505326  [UniProt]  [KEGG]putative membrane protein
31pilU4433025..4433687 [+], 66316505327  [UniProt]  [KEGG]prepilin peptidase
32pilV4433684..4434991 [+], 130816505328  [UniProt]  [KEGG]prepilinVF
33'pilV24434993..4435253 [-], 26116505329  [UniProt]  [KEGG]prepilin, alternative C-terminal region
34rci4435339..4436490 [+], 115216505330  [UniProt]  [KEGG]shufflon-specific DNA recombinase
35pilK4436587..4437054 [+], 46816505331  [UniProt]  [KEGG]putative exported protein
36STY45544437266..4438141 [+], 87616505332  [UniProt]  [KEGG]hypothetical protein
37STY45574438648..4439562 [+], 91516505333  [UniProt]  [KEGG]putative membrane protein
38STY45584439581..4440321 [+], 74116505334  [UniProt]  [KEGG]putative exported protein
39STY45594440435..4440986 [+], 55216505335  [UniProt]  [KEGG]hypothetical protein
40STY45604441022..4441522 [+], 50116505336  [UniProt]  [KEGG]hypothetical protein
41STY45614441532..4442101 [+], 57016505337  [UniProt]  [KEGG]putative membrane protein
42STY45624442121..4444211 [+], 209116505338  [UniProt]  [KEGG]hypothetical protein
43STY45634444208..4444966 [+], 75916505339  [UniProt]  [KEGG]putative membrane protein
44STY45644445185..4445457 [+], 27316505340  [UniProt]  [KEGG]hypothetical protein
45STY45654445457..4445696 [+], 24016505341  [UniProt]  [KEGG]putative membrane protein
46STY45664445726..4446088 [+], 36316505342  [UniProt]  [KEGG]putative membrane protein
47STY45684446469..4447122 [+], 65416505343  [UniProt]  [KEGG]possible exported protein
48STY45694447122..4448021 [+], 90016505344  [UniProt]  [KEGG]hypothetical protein
49STY45704448011..4449489 [+], 147916505345  [UniProt]  [KEGG]putative exported protein
50STY45714449482..4449925 [+], 44416505346  [UniProt]  [KEGG]putative lipoprotein
51STY45724449922..4450341 [+], 42016505347  [UniProt]  [KEGG]hypothetical protein
52STY45734450338..4452761 [+], 242416505348  [UniProt]  [KEGG]hypothetical protein
53STY45744452916..4453302 [+], 38716505349  [UniProt]  [KEGG]hypothetical protein
54STY45754453457..4453849 [+], 39316505350  [UniProt]  [KEGG]hypothetical protein
55STY45764453846..4454814 [+], 96916505351  [UniProt]  [KEGG]hypothetical protein
56STY45774454829..4456259 [+], 143116505352  [UniProt]  [KEGG]hypothetical protein
57STY45784456256..4456588 [+], 33316505353  [UniProt]  [KEGG]putative membrane protein
58STY45794456592..4458097 [+], 150616505354  [UniProt]  [KEGG]putative membrane protein
59STY45804458133..4458522 [-], 39016505355  [UniProt]  [KEGG]putative membrane protein
60STY45824458746..4459105 [-], 36016505356  [UniProt]  [KEGG]possible exported protein
61STY45834459393..4460640 [+], 124816505357  [UniProt]  [KEGG]conserved hypothetical proteinVF
62STY45844460652..4461266 [+], 61516505358  [UniProt]  [KEGG]conserved hypothetical proteinVF
63STY45854461477..4462019 [-], 54316505359  [UniProt]  [KEGG]hypothetical protein
64STY45864463285..4464205 [+], 92116505360  [UniProt]  [KEGG]hypothetical protein
65STY45874464722..4465231 [+], 51016505361  [UniProt]  [KEGG]hypothetical protein
66STY45884465327..4465707 [+], 38116505362  [UniProt]  [KEGG]hypothetical protein
67STY45894466173..4466757 [+], 58516505363  [UniProt]  [KEGG]hypothetical protein
68STY45904466754..4467050 [+], 29716505364  [UniProt]  [KEGG]hypothetical protein
69STY45914467128..4467586 [+], 45916505365  [UniProt]  [KEGG]hypothetical protein
70STY45924467675..4469624 [+], 195016505366  [UniProt]  [KEGG]hypothetical proteinVF
71STY45934469696..4470604 [+], 90916505367  [UniProt]  [KEGG]hypothetical protein
72STY45944470678..4471577 [+], 90016505368  [UniProt]  [KEGG]hypothetical protein
73STY45954471619..4471978 [+], 36016505369  [UniProt]  [KEGG]conserved hypothetical protein
74STY45964472078..4472347 [-], 27016505371  [UniProt]  [KEGG]hypothetical protein
75samB4472479..4473753 [-], 127516505372  [UniProt]  [KEGG]UV protection protein
76samA4473753..4507730 [-], 33978pseudogene UV protection protein (pseudogene)
77STY45994473973..4474350 [+], 37816505373  [UniProt]  [KEGG]hypothetical protein
78STY46004474437..4474655 [-], 21916505374  [UniProt]  [KEGG]putative positive regulator of late gene transcription
79STY46014474723..4475823 [-], 110116505375  [UniProt]  [KEGG]putative regulator of late gene expression
80STY46024475820..4476305 [-], 48616505376  [UniProt]  [KEGG]putative phage tail protein
81STY46034476305..4479085 [-], 278116505377  [UniProt]  [KEGG]hypothetical protein
82STY46044479078..4479197 [-], 12016505378  [UniProt]  [KEGG]hypothetical protein
83STY46054479212..4479514 [-], 30316505379  [UniProt]  [KEGG]putative phage tail protein
84STY46064479569..4480084 [-], 51616505380  [UniProt]  [KEGG]probable major tail tube protein
85STY46074480094..4481266 [-], 117316505381  [UniProt]  [KEGG]probable major tail sheath protein
86'pin4481369..4481590 [-], 222pseudogene DNA-invertase (pseudogene)
87sopE4481801..4482523 [+], 72316505382  [UniProt]  [KEGG]invasion-associated secreted protein.VF
88STY46104482721..4483128 [-], 40816505383  [UniProt]  [KEGG]putative phage tail fibre protein
89STY46114483135..4484754 [-], 162016505384  [UniProt]  [KEGG]probable phage tail fibre protein
90STY46124484751..4485356 [-], 60616505385  [UniProt]  [KEGG]putative phage tail protein
91STY46134485349..4486257 [-], 90916505386  [UniProt]  [KEGG]probable phage baseplate assembly protein
92STY46144486244..4486603 [-], 36016505387  [UniProt]  [KEGG]phage baseplate assembly protein
93STY46154486600..4487178 [-], 57916505388  [UniProt]  [KEGG]putative phage baseplate assembly protein
94STY46164487247..4487693 [-], 44716505389  [UniProt]  [KEGG]putative phage tail completion protein
95STY46174487686..4488117 [-], 43216505390  [UniProt]  [KEGG]putative phage tail protein
96STY46184488213..4488638 [-], 42616505391  [UniProt]  [KEGG]putative regulatory protein
97STY46194488638..4489015 [-], 37816505392  [UniProt]  [KEGG]putative membrane protein
98nucD24489020..4489490 [-], 47116505393  [UniProt]  [KEGG]putative lysozyme
99nucE24489510..4489725 [-], 21616505394  [UniProt]  [KEGG]possible secretion protein
100STY46224489729..4489932 [-], 20416505395  [UniProt]  [KEGG]putative phage tail protein
101STY46234489932..4490396 [-], 46516505396  [UniProt]  [KEGG]putative capsid completion protein
102STY46244490490..4491140 [-], 65116505397  [UniProt]  [KEGG]putative phage terminase
103STY46254491144..4492208 [-], 106516505398  [UniProt]  [KEGG]putative major capsid protein
104STY46264492225..4493058 [-], 83416505399  [UniProt]  [KEGG]putative capsid protein
105STY46274493201..4494967 [+], 176716505400  [UniProt]  [KEGG]probable terminase subunit
106STY46284494964..4496010 [+], 104716505401  [UniProt]  [KEGG]probable capsid portal protein
107STY46294496059..4496754 [-], 69616505402  [UniProt]  [KEGG]hypothetical protein
108STY46304496774..4497838 [-], 106516505403  [UniProt]  [KEGG]hypothetical protein
109STY46314497835..4498899 [-], 106516505404  [UniProt]  [KEGG]hypothetical protein
110STY46324498909..4499127 [-], 21916505405  [UniProt]  [KEGG]hypothetical protein
111STY46334499226..4499656 [-], 431pseudogene SOS operon tum protein (pseudogene)
112STY46354499824..4502238 [-], 241516505406  [UniProt]  [KEGG]conserved hypothetical protein
113STY46364502229..4503089 [-], 86116505407  [UniProt]  [KEGG]DNA adenine methylase
114STY46374503086..4503670 [-], 58516505408  [UniProt]  [KEGG]putative exonuclease
115STY46384503667..4503894 [-], 22816505409  [UniProt]  [KEGG]hypothetical protein
116STY46394503894..4504127 [-], 23416505410  [UniProt]  [KEGG]hypothetical protein
117STY46404504195..4504536 [-], 34216505411  [UniProt]  [KEGG]conserved hypothetical protein
118STY46414504500..4504700 [-], 20116505412  [UniProt]  [KEGG]hypothetical protein
119cII4504708..4505217 [-], 51016505413  [UniProt]  [KEGG]phage regulatory protein
120apl4505250..4505492 [-], 24316505414  [UniProt]  [KEGG]phage regulatory protein
121cI4505609..4506241 [+], 63316505415  [UniProt]  [KEGG]phage repressor protein cI
122STY46454506245..4507270 [+], 102616505416  [UniProt]  [KEGG]phage integraseVF
123STY46474507998..4508111 [+], 11416505417  [UniProt]  [KEGG]hypothetical protein
124STY46484508347..4508634 [+], 28816505418  [UniProt]  [KEGG]hypothetical protein
125STY46494508645..4509535 [+], 89116505419  [UniProt]  [KEGG]Putative methyltransferase
126yjhP4509535..4510281 [+], 74716505420  [UniProt]  [KEGG]conserved hypothetical protein
127vexE4510583..4512553 [-], 197116505421  [UniProt]  [KEGG]Vi polysaccharide export proteinVF
128vexD4512573..4513877 [-], 130516505422  [UniProt]  [KEGG]Vi polysaccharide export inner-membrane proteinVF
129vexC4513900..4514595 [-], 69616505423  [UniProt]  [KEGG]Vi polysaccharide export ATP-binding proteinVF
130vexB4514621..4515415 [-], 79516505424  [UniProt]  [KEGG]Vi polysaccharide export inner-membrane protein (ABC-2 type transporter)VF
131vexA4515425..4516492 [-], 106816505425  [UniProt]  [KEGG]Vi polysaccharide export proteinVF
132tviE4516537..4518273 [-], 173716505426  [UniProt]  [KEGG]Vi polysaccharide biosynthesis protein TviE, Glycosyl transferases group 1VF
133insB4518289..4518792 [-], 50416505427  [UniProt]  [KEGG]insertion element IS1 protein InsBVF
134insA4518711..4518986 [-], 27616505428  [UniProt]  [KEGG]insertion element IS1 proteinVF
135tviD4519050..4521545 [-], 249616505429  [UniProt]  [KEGG]Vi polysaccharide biosynthesis proteinVF
136tviC4521569..4522615 [-], 104716505430  [UniProt]  [KEGG]Vi polysaccharide biosynthesis protein, epimeraseVF
137tviB4522618..4523895 [-], 127816505431  [UniProt]  [KEGG]Vi polysaccharide biosynthesis protein, UDP-glucose/GDP-mannose dehydrogenaseVF
138tviA4524140..4524679 [-], 54016505432  [UniProt]  [KEGG]Vi polysaccharide biosynthesis proteinVF
139STY46634525220..4525408 [+], 18916505433  [UniProt]  [KEGG]hypothetical protein
140STY46644525533..4527044 [+], 151216505434  [UniProt]  [KEGG]putative DNA helicase
141STY46654527028..4528617 [+], 159016505435  [UniProt]  [PDB]  [KEGG]hypothetical protein
142STY46664528781..4529794 [+], 101416505436  [UniProt]  [KEGG]probable phage integrase
143STY46674530221..4530514 [+], 29416505437  [UniProt]  [KEGG]hypothetical proteinTA
144STY46684530511..4530999 [+], 48916505438  [UniProt]  [KEGG]conserved hypothetical proteinTA
145STY46694531179..4531631 [-], 45316505439  [UniProt]  [KEGG]putative membrane protein
146STY46704532268..4534553 [-], 228616505440  [UniProt]  [KEGG]hypothetical protein
147STY46714534634..4536307 [-], 167416505441  [UniProt]  [KEGG]putative membrane protein
148STY46724536854..4537315 [+], 46216505442  [UniProt]  [KEGG]hypothetical protein
149cII4537312..4537533 [+], 22216505443  [UniProt]  [KEGG]transcriptional regulatory protein
150STY46744537567..4537710 [-], 14416505444  [UniProt]  [KEGG]hypothetical protein
151STY46754537926..4538252 [-], 32716505445  [UniProt]  [KEGG]hypothetical protein
152STY46764538390..4539172 [+], 78316505446  [UniProt]  [KEGG]hypothetical protein
153STY46774539197..4539409 [-], 21316505447  [UniProt]  [KEGG]putative membrane protein
154int4539799..4540077 [-], 27916505448  [UniProt]  [KEGG]integrase (fragment)VF
155STY46794540153..4541343 [-], 119116505449  [UniProt]  [KEGG]putative membrane protein
156int4541654..4542913 [-], 126016505450  [UniProt]  [KEGG]bacteriophage integraseVF
157STY46814543264..4543839 [-], 57616505451 putative transcriptional regulator
158dsbD4543876..4545579 [-], 170416505452 thiol:disulfide interchange protein DsbD
159cutA4545555..4545902 [-], 34816505453 periplasmic divalent cation tolerance protein CutA
160dcuA4546023..4547324 [-], 130216505454 anaerobic C4-dicarboxylate transporter
 
flank Flanking regions
integrase Gene may contribute to site-specific recombination
conjugation Gene may play role in conjugative transfer

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