I. Summary

SecReT6 ID	24
Strain	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_003198
Location	296922..336058
Comment
Function	N/A
T6SS Type	Type i; subtype i3
Bioinformatics investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	1	1	1	1	2	1	0	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	0

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	STY0276 (dkgB)	292894..293697 [+], 804	16759241	2,5-diketo-D-gluconate reductase B
2	STY0277 (yafC)	293718..294632 [-], 915	16759242	transcriptional regulator
3	STY0278	294737..295912 [+], 1176	16759243	drug efflux protein
4	STY0279 (yafD)	296065..296844 [+], 780	16759244	hypothetical protein
5	STY0280 (yafE)	296922..297692 [+], 771	16759245	methyltransferase
6	STY0281 (mltD)	297748..299115 [-], 1368	16759246	membrane-bound lytic murein transglycosylase D
7	STY0282 (gloB)	299187..299942 [-], 756	16759247	hydroxyacylglutathione hydrolase
8	STY0283	299977..300699 [+], 723	16759248	hypothetical protein
9	STY0284 (rnhA)	300696..301163 [-], 468	16759249	ribonuclease H
10	STY0285 (dnaQ)	301227..301958 [+], 732	16759250	DNA polymerase III subunit epsilon
11	STY0286	302488..303120 [-], 633	16759251	hypothetical protein	TssA
12	STY0287	303120..303542 [-], 423	16759252	hypothetical protein	TssA
13	STY0288	303553..304548 [-], 996	16759253	hypothetical protein	TssG
14	STY0289	304545..306428 [-], 1884	16759254	hypothetical protein	TssF
15	STY0290	306444..306938 [-], 495	16759255	hypothetical protein	TssE
16	STY0291	306935..307759 [-], 825	16759256	hypothetical protein	TagJ
17	STY0292	307746..308648 [-], 903	16759257	hypothetical protein
18	STY0294	309016..311679 [+], 2664	16759259	ClpB-like protein	TssH
19	STY0295	311664..311762 [+], 99	16759260	hypothetical protein
20	STY0296	311765..312055 [+], 291	16759261	hypothetical protein
21	STY0297	312119..312661 [+], 543	16759262	hypothetical protein	TssB
22	STY0300	314246..314647 [+], 402	16759263	hypothetical protein	STY0300 (e)
23	STY0301	314619..315044 [+], 426	16759264	hypothetical protein	STY0301 (i)
24	STY0302	315281..315766 [+], 486	16759265	hypothetical protein	TssD
25	STY0303	315833..316369 [+], 537	16759266	lipoprotein	TssJ
26	STY0304	316373..317716 [+], 1344	16759267	hypothetical protein	TssK
27	STY0305	317713..319014 [+], 1302	16759268	hypothetical protein	TssL
28	STY0306	319019..319768 [+], 750	16759269	hypothetical protein
29	STY0307	319800..320294 [+], 495	16759270	hypothetical protein
30	STY0310	324392..325159 [+], 768	16759271	hypothetical protein
31	STY0311	325202..325672 [+], 471	16759272	hypothetical protein
32	STY0312	325657..326130 [+], 474	16759273	hypothetical protein
33	STY0313	326234..326704 [+], 471	16759274	hypothetical protein
34	STY0314	326689..327150 [+], 462	16759275	hypothetical protein
35	STY0316	327278..327694 [+], 417	16759276	hypothetical protein
36	STY0317	327721..328158 [+], 438	16759277	hypothetical protein
37	STY0318	328166..328273 [+], 108	16759278	hypothetical protein
38	STY0319	328636..330825 [+], 2190	16759279	Rhs-family protein	TssI
39	STY0320	330849..331295 [+], 447	16759280	hypothetical protein
40	STY0321	331314..335378 [+], 4065	16759281	Rhs-family protein	PAAR
41	STY0322	335381..336058 [+], 678	16759282	hypothetical protein
42	STY0323	336077..336370 [+], 294	16759283	hypothetical protein
43	STY0324	336466..338997 [+], 2532	16759284	Rhs-family protein
44	STY0326	339076..339336 [+], 261	16759285	hypothetical protein
45	STY0327	339338..339781 [+], 444	16759286	hypothetical protein
46	STY0328	339851..340156 [-], 306	16759287	hypothetical protein

 Genes in the 5-kb flanking regions if available, or non-core components encoded by the T6SS gene cluster if any. In the 'Note' column,if available, '(e)' denotes effector while '(i)' for immunity protein

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Proteins        Genes

V. Investigation of the genomic context of the T6SS gene cluster.

1. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the mobile genetic elements database, ACLAME.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

Homology Effector list

STY0300 , SciK, STY2606, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	STY0300	314246..314647 [+], 402	16759263	hypothetical protein	STY0300
2	STY0302	315281..315766 [+], 486	16759265	hypothetical protein	SciK
3	STY2606	2441934..2442302 [+], 369	16761300	hypothetical protein	STY2606
4	STY3300	3146822..3147307 [-], 486	16761909	hypothetical protein	Hcp

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Proteins        Genes

Homology Immunity protein list

STY0301, STY2607

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog

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Proteins        Genes

(1) Blondel CJ et al. (2009). Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes. BMC Genomics. 10:354. [PudMed:19653904]

(2) Boyer F et al. (2009). Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources. BMC Genomics. 10:104. [PudMed:19284603]

This literature contains bioinformatics investigation