I. Summary

SecReT6 ID	560
Strain	Salmonella enterica subsp. enterica serovar Typhimurium str. 798
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_017046
Location	304654..332036
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	UMN798_0284 (mltD)	299912..301132 [-], 1221	383495078	membrane-bound lytic murein transglycosylase d precursor
2	UMN798_0285 (gloB)	301351..302106 [-], 756	383495079	hydroxyacylglutathione hydrolase
3	UMN798_0286	302195..302863 [+], 669	383495080	hypothetical protein
4	UMN798_0287 (rnhA)	302860..303327 [-], 468	383495081	ribonuclease H
5	UMN798_0288 (dnaQ)	303382..304122 [+], 741	383495082	DNA polymerase III subunit epsilon
6	UMN798_0290 (sciA)	304654..305703 [-], 1050	383495083	SPI-6 associated protein	TssA
7	UMN798_0291 (sciB)	305720..306715 [-], 996	383495084	SPI-6 associated protein	TssG
8	UMN798_0292 (sciC)	306712..308595 [-], 1884	383495085	SPI-6 associated protein	TssF
9	UMN798_0293 (sciD)	308611..309105 [-], 495	383495086	SPI-6 associated protein	TssE
10	UMN798_0294 (sciE)	309102..309926 [-], 825	383495087	SPI-6 associated protein	TagJ
11	UMN798_0295 (sciF)	309913..310815 [-], 903	383495088	SPI-6 associated protein
12	UMN798_0296 (sciG)	311183..313822 [+], 2640	383495089	SPI-6 associated protein	TssH
13	UMN798_0297 (sciH)	313922..314464 [+], 543	383495090	SPI-6 associated protein	TssB
14	UMN798_0298 (sciI)	314488..315981 [+], 1494	383495091	SPI-6 associated protein	TssC
15	UMN798_0300 (sciK)	316867..317352 [+], 486	383495092	SPI-6 associated protein	TssD
16	UMN798_0301	317702..318142 [+], 441	383495093	SPI-6 associated protein	STM0277 (e)
17	UMN798_0302	318178..318510 [+], 333	383495094	SPI-6 associated protein	STM0278 (i)
18	UMN798_0303 (sciK1)	318653..319138 [+], 486	383495095	SPI-6 associated protein	TssD
19	UMN798_0304 (sciN)	319250..319741 [+], 492	383495096	lipoprotein (SPI-6 associated)	TssJ
20	UMN798_0305 (sciO)	319745..321088 [+], 1344	383495097	SPI-6 associated protein	TssK
21	UMN798_0306 (sciP)	321085..322389 [+], 1305	383495098	membrane protein (SPI-6 associated)	TssL
22	UMN798_0307 (sciQ)	322394..323167 [+], 774	383495099	membrane protein, virulence associated protein
23	UMN798_0308 (sciR)	323445..323801 [+], 357	383495100	SPI-6 associated protein
24	UMN798_0309 (sciS)	323835..327704 [+], 3870	383495101	IcmF-related integral membrane ATP-binding protein, virulence associated protein	TssM
25	UMN798_0310 (sciT)	327719..328492 [+], 774	383495102	SPI-6 associated protein
26	UMN798_0311 (sciU)	328489..328905 [+], 417	383495103	hypothetical protein
27	UMN798_0312 (sciV)	328929..329450 [+], 522	383495104	SPI-6 associated protein
28	UMN798_0314 (vrgS)	329847..332036 [+], 2190	383495105	type VI secretion protein	TssI
29	UMN798_0315 (sciW)	332060..332506 [+], 447	383495106	SPI-6 associated protein
30	UMN798_0316	332525..333820 [+], 1296	383495107	Rhs-family protein (SPI-6 associated)	PAAR
31	UMN798_0317	333833..336121 [+], 2289	383495108	Rhs-family protein (SPI-6 associated)
32	UMN798_0318	336115..336378 [+], 264	383495109	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, Hcp

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	UMN798_0300(sciK)	316867..317352 [+], 486	383495092	SPI-6 associated protein	SciK
2	UMN798_0301	317702..318142 [+], 441	383495093	SPI-6 associated protein	STM0277
3	UMN798_0303(sciK1)	318653..319138 [+], 486	383495095	SPI-6 associated protein	SciK
4	UMN798_3404	3310777..3311262 [-], 486	383497791	hypothetical 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	UMN798_0302	318178..318510 [+], 333	383495094	SPI-6 associated protein	STM0278
2	UMN798_2563	2484363..2484881 [+], 519	383497076	lipoprotein	STY2607

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Proteins        Genes

N/A