I. Summary

SecReT6 ID	85
Strain	Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_006905
Location	295006..331820
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	0	1	1	1	1	1	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	1

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	SC0251 (dkgB)	290977..291780 [+], 804	62178821	2,5-diketo-D-gluconate reductase B
2	SC0252 (yafC)	291802..292716 [-], 915	62178822	LysR family transcriptional regulator
3	SC0253 (ydhP)	292821..293996 [+], 1176	62178823	drug efflux protein
4	SC0254 (yafD)	294128..294928 [+], 801	62178824	hypothetical protein
5	SC0255 (yafE)	295006..295776 [+], 771	62178825	methyltransferase in menaquinone/biotin biosynthesis
6	SC0256 (mltD)	295832..297199 [-], 1368	62178826	membrane-bound lytic murein transglycosylase D
7	SC0257 (gloB)	297271..298026 [-], 756	62178827	hydroxyacylglutathione hydrolase
8	SC0258 (yafS)	298061..298783 [+], 723	62178828	hypothetical protein
9	SC0259 (rnhA)	298780..299247 [-], 468	162139612	ribonuclease H
10	SC0260 (dnaQ)	299302..300042 [+], 741	62178830	DNA polymerase III subunit epsilon
11	SC0261	300574..301629 [-], 1056	62178831	hypothetical protein	TssA
12	SC0262	301640..302635 [-], 996	62178832	hypothetical protein	TssG
13	SC0263	302632..304515 [-], 1884	62178833	hypothetical protein	TssF
14	SC0264	304531..305025 [-], 495	62178834	hypothetical protein	TssE
15	SC0265	305022..305771 [-], 750	62178835	hypothetical protein	TagJ
16	SC0266	305833..306735 [-], 903	62178836	hypothetical protein
17	SC0268	309841..310383 [+], 543	62178838	hypothetical protein	TssB
18	SC0269 (sirA)	310407..311915 [+], 1509	62178839	hypothetical protein	TssC
19	SC0270	311982..312368 [+], 387	62178840	hypothetical protein
20	SC0271	312381..312827 [+], 447	62178841	hypothetical protein
21	SC0272	313079..313564 [+], 486	62178842	hypothetical protein	TssD
22	SC0273	313631..314167 [+], 537	62178843	outer membrane lipoprotein	TssJ
23	SC0274	314171..315514 [+], 1344	62178844	hypothetical protein	TssK
24	SC0275	315511..316815 [+], 1305	62178845	hypothetical protein	TssL
25	SC0276	316820..317593 [+], 774	62178846	inner membrane protein
26	SC0277	317783..318226 [+], 444	62178847	shiga-like toxin A subunit
27	SC0278	318260..322129 [+], 3870	62178848	inner membrane protein	TssM
28	SC0279	322129..322917 [+], 789	62178849	hypothetical protein
29	SC0280	322914..323330 [+], 417	62178850	hypothetical protein
30	SC0281	323354..323875 [+], 522	62178851	hypothetical protein
31	SC0282	324271..326505 [+], 2235	62178852	Rhs-family protein	TssI
32	SC0283	326517..327023 [+], 507	62178853	hypothetical protein
33	SC0284 (rhs)	327039..331820 [+], 4782	62178854	Rhs-family protein	PAAR
34	SC0285	331839..332147 [+], 309	62178855	hypothetical protein
35	SC0286 (yjiW)	332206..332463 [-], 258	62178856	hypothetical protein
36	SC0287	333900..334367 [+], 468	62178857	hypothetical protein
37	SC0288	334610..334963 [+], 354	62178858	hypothetical protein
38	SC0289	335030..335344 [-], 315	62178859	hypothetical protein
39	SC0290	335477..335617 [-], 141	62178860	hypothetical protein
40	SC0291	335820..336101 [+], 282	62178861	integrase core subunit

 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

SciK , STY2606, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SC0272	313079..313564 [+], 486	62178842	hypothetical protein	SciK
2	SC2377	2501325..2501693 [+], 369	62180947	hypothetical protein	STY2606
3	SC3071	3250460..3250945 [-], 486	62181641	hypothetical protein	Hcp

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Proteins        Genes

Homology Immunity protein list

STY2607

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SC2378	2501693..2502211 [+], 519	62180948	hypothetical protein	STY2607

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Proteins        Genes

(1) 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