I. Summary

SecReT6 ID	552
Strain	Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_016857
Location	304656..332038
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	2	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	STM474_0271 (mltD)	299914..301281 [-], 1368	379699476	membrane-bound lytic murein transglycosylase D
2	STM474_0272	301353..302108 [-], 756	379699477	putative periplasmic fimbrial chaperone
3	STM474_0273 (yafS)	302143..302865 [+], 723	379699478	putative SAM-dependent methyltransferase
4	STM474_0274 (rnhA)	302862..303329 [-], 468	379699479	ribonuclease H
5	STM474_0275 (dnaQ)	303384..304124 [+], 741	379699480	DNA polymerase III subunit epsilon
6	STM474_0277	304656..305711 [-], 1056	379699481	putative cytoplasmic protein	TssA
7	STM474_0278	305722..306717 [-], 996	379699482	putative cytoplasmic protein	TssG
8	STM474_0279 (vasA)	306714..308597 [-], 1884	379699483	type VI secretion protein	TssF
9	STM474_0280	308613..309107 [-], 495	379699484	putative cytoplasmic protein	TssE
10	STM474_0281 (sciE)	309104..309943 [-], 840	379699485	SciE protein	TagJ
11	STM474_0282	309915..310817 [-], 903	379699486	putative cytoplasmic protein
12	STM474_0283	311185..313824 [+], 2640	379699487	putative chaperone ATPase	TssH
13	STM474_0284	313924..314466 [+], 543	379699488	putative cytoplasmic protein	TssB
14	STM474_0285	314490..315983 [+], 1494	379699489	SciI protein	TssC
15	STM474_0286	316046..316156 [+], 111	379699490	invasol SirA
16	STM474_0287	316169..316615 [+], 447	379699491	putative cytoplasmic protein
17	STM474_0288	316869..317354 [+], 486	379699492	hypothetical protein	TssD
18	STM474_0289	317659..318144 [+], 486	379699493	putative cytoplasmic protein	STM0277 (e)
19	STM474_0290	318129..318512 [+], 384	379699494	hypothetical protein	STM0278 (i)
20	STM474_0291	318655..319140 [+], 486	379699495	putative cytoplasmic protein	TssD
21	STM474_0292	319207..319743 [+], 537	379699496	putative outer membrane lipoprotein	TssJ
22	STM474_0293	319747..321090 [+], 1344	379699497	hypothetical protein	TssK
23	STM474_0294	321087..322391 [+], 1305	379699498	Putative outer membrane protein, OmpA family	TssL
24	STM474_0295	322396..323169 [+], 774	379699499	putative inner membrane protein
25	STM474_0296 (sciR)	323360..323803 [+], 444	379699500	SciR protein
26	STM474_0297 (sciS)	323837..327706 [+], 3870	379699501	SciS protein	TssM
27	STM474_0298	327706..328494 [+], 789	379699502	putative cytoplasmic protein
28	STM474_0299	328491..328907 [+], 417	379699503	hypothetical protein
29	STM474_0300	328931..329452 [+], 522	379699504	putative cytoplasmic protein
30	STM474_0301	329849..332038 [+], 2190	379699505	Rhs-family protein	TssI
31	STM474_0302	332062..332508 [+], 447	379699506	hypothetical protein
32	STM474_0303 (rhs1)	332521..336123 [+], 3603	379699507	Rhs1 protein	PAAR

 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 , STM0277, SciK, STY2606, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	STM474_0288	316869..317354 [+], 486	379699492	hypothetical protein	SciK
2	STM474_0289	317659..318144 [+], 486	379699493	putative cytoplasmic protein	STM0277
3	STM474_0291	318655..319140 [+], 486	379699495	putative cytoplasmic protein	SciK
4	STM474_2474	2484631..2484999 [+], 369	379701609	putative cytoplasmic protein	STY2606
5	STM474_3280	3311675..3312160 [-], 486	379702388	putative cytoplasmic protein	Hcp

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Proteins        Genes

Homology Immunity protein list

STM0278, STY2607

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	STM474_0290	318129..318512 [+], 384	379699494	hypothetical protein	STM0278
2	STM474_2475	2484999..2485517 [+], 519	379701610	hypothetical protein	STY2607

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Proteins        Genes

N/A