I. Summary

SecReT6 ID	553
Strain	Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_016860
Location	304666..332063
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	STMDT12_C02560 (mltD)	299924..301144 [-], 1221	378982797	membrane-bound lytic murein transglycosylase D
2	STMDT12_C02570	301363..302118 [-], 756	378982798	hydroxyacylglutathione hydrolase
3	STMDT12_C02580	302153..302875 [+], 723	378982799	putative methyltransferase
4	STMDT12_C02590 (rnhA)	302872..303339 [-], 468	378982800	ribonuclease H
5	STMDT12_C02600	303394..304134 [+], 741	378982801	DNA polymerase III subunit epsilon
6	STMDT12_C02610	304468..304575 [+], 108	378982802	hypothetical protein
7	STMDT12_C02620	304666..305715 [-], 1050	378982803	ImpA-related N- family protein	TssA
8	STMDT12_C02630	305732..306727 [-], 996	378982804	putative cytoplasmic protein	TssG
9	STMDT12_C02640	306724..308607 [-], 1884	378982805	hypothetical protein	TssF
10	STMDT12_C02650	308623..309117 [-], 495	378982806	putative cytoplasmic protein	TssE
11	STMDT12_C02660	309114..309938 [-], 825	378982807	putative cytoplasmic protein	TagJ
12	STMDT12_C02670	309925..310827 [-], 903	378982808	putative cytoplasmic protein
13	STMDT12_C02680	311195..313834 [+], 2640	378982809	putative chaperone ATPase	TssH
14	STMDT12_C02690	313934..314476 [+], 543	378982810	type VI secretion protein	TssB
15	STMDT12_C02700	314500..316008 [+], 1509	378982811	SciI protein	TssC
16	STMDT12_C02710	316894..317379 [+], 486	378982812	hemolysin-coregulated protein	TssD
17	STMDT12_C02720	317684..318169 [+], 486	378982813	putative cytoplasmic protein	STM0277 (e)
18	STMDT12_C02730	318205..318537 [+], 333	378982814	hypothetical protein	STM0278 (i)
19	STMDT12_C02740	318680..319165 [+], 486	378982815	hemolysin-coregulated protein	TssD
20	STMDT12_C02750	319232..319768 [+], 537	378982816	putative outer membrane lipoprotein	TssJ
21	STMDT12_C02760	319772..321115 [+], 1344	378982817	type VI secretion protein	TssK
22	STMDT12_C02770	321112..322416 [+], 1305	378982818	hypothetical protein	TssL
23	STMDT12_C02780	322421..323194 [+], 774	378982819	putative inner membrane protein
24	STMDT12_C02790	323472..323828 [+], 357	378982820	putative Shiga-like toxin A subunit
25	STMDT12_C02800	323862..327731 [+], 3870	378982821	putative inner membrane protein	TssM
26	STMDT12_C02810	327731..328519 [+], 789	378982822	putative cytoplasmic protein
27	STMDT12_C02820	328516..328932 [+], 417	378982823	hypothetical protein
28	STMDT12_C02830	328959..329477 [+], 519	378982824	pathogenicity island protein
29	STMDT12_C02840	329874..332063 [+], 2190	378982825	putative cytoplasmic protein	TssI
30	STMDT12_C02850	332087..332533 [+], 447	378982826	hypothetical protein
31	STMDT12_C02860	332552..336646 [+], 4095	378982827	putative RHS-like protein	PAAR
32	STMDT12_C02870	336640..336903 [+], 264	378982828	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

SciK , STM0277, SciK, STY2606, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	STMDT12_C02710	316894..317379 [+], 486	378982812	hemolysin-coregulated protein	SciK
2	STMDT12_C02720	317684..318169 [+], 486	378982813	putative cytoplasmic protein	STM0277
3	STMDT12_C02740	318680..319165 [+], 486	378982815	hemolysin-coregulated protein	SciK
4	STMDT12_C23970	2482458..2482826 [+], 369	378984938	putative cytoplasmic protein	STY2606
5	STMDT12_C31850	3314236..3314721 [-], 486	378985725	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	STMDT12_C02730	318205..318537 [+], 333	378982814	hypothetical protein	STM0278
2	STMDT12_C23980	2482826..2483344 [+], 519	378984939	putative lipoprotein	STY2607

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Proteins        Genes

N/A