I. Summary

SecReT6 ID	857
Strain	Salmonella enterica subsp. enterica serovar Typhimurium str. DT2
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_022544
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

14

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	STMDT2_02561 (mltD)	299912..301279 [-], 1368	549722978	membrane-bound lytic murein transglycosylase d precursor
2	STMDT2_02571 (gloB)	301351..302106 [-], 756	549722979	7 probable hydroxyacylglutathione hydrolase
3	STMDT2_02581	302141..302863 [+], 723	549722980	hypothetical protein
4	STMDT2_02591 (rnhA)	302860..303327 [-], 468	549722981	ribonuclease H
5	STMDT2_02601 (dnaQ)	303391..304122 [+], 732	549722982	DNA polymerase III epsilon subunit
6	STMDT2_02611 (sciA)	304654..305709 [-], 1056	549722983	virulence associated protein	TssA
7	STMDT2_02621 (sciB)	305720..306715 [-], 996	549722984	virulence associated protein	TssG
8	STMDT2_02631 (sciC)	306712..308595 [-], 1884	549722985	virulence associated protein	TssF
9	STMDT2_02641 (sciD)	308611..309105 [-], 495	549722986	virulence associated protein	TssE
10	STMDT2_02651 (sciE)	309102..309926 [-], 825	549722987	virulence associated protein	TagJ
11	STMDT2_02661 (sciF)	309913..310815 [-], 903	549722988	virulence associated protein
12	STMDT2_02671 (sciG)	311183..313822 [+], 2640	549722989	virulence associated protein	TssH
13	STMDT2_02681 (sciH)	313922..314464 [+], 543	549722990	virulence associated protein	TssB
14	STMDT2_02691 (sciI)	314488..315981 [+], 1494	549722991	virulence associated protein	TssC
15	STMDT2_02701	315996..316154 [+], 159	549722992	hypothetical protein
16	STMDT2_02711	316167..316613 [+], 447	549722993	hypothetical protein
17	STMDT2_02721 (sciK)	316867..317352 [+], 486	549722994	virulence associated protein	TssD
18	STMDT2_02731	317657..318142 [+], 486	549722995	hypothetical protein	STM0277 (e)
19	STMDT2_02741	318127..318510 [+], 384	549722996	hypothetical protein	STM0278 (i)
20	STMDT2_02751 (sciK1)	318653..319138 [+], 486	549722997	virulence associated protein	TssD
21	STMDT2_02761 (sciN)	319205..319741 [+], 537	549722998	hypothetical protein	TssJ
22	STMDT2_02771 (sciO)	319745..321088 [+], 1344	549722999	virulence associated protein	TssK
23	STMDT2_02781 (sciP)	321085..322389 [+], 1305	549723000	putative membrane protein, virulence associated protein	TssL
24	STMDT2_02791 (sciQ)	322394..323167 [+], 774	549723001	putative membrane protein, virulence associated protein
25	STMDT2_02801	323370..323801 [+], 432	549723002	hypothetical protein
26	STMDT2_02811 (sciS)	323835..327704 [+], 3870	549723003	probable IcmF-related integral membrane ATP-binding protein, virulence associated protein	TssM
27	STMDT2_02821	327704..328492 [+], 789	549723004	hypothetical protein
28	STMDT2_02831 (sciU)	328489..328905 [+], 417	549723005	virulence associated,probable secreted protein
29	STMDT2_02841	328929..329450 [+], 522	549723006	conserved hypothetical pathogenicity island protein
30	STMDT2_02851 (vrgS)	329847..332036 [+], 2190	549723007	Type VI secretion protein	TssI
31	STMDT2_02861 (sciW)	332060..332506 [+], 447	549723008	virulence associated protein
32	STMDT2_02862	332519..336619 [+], 4101	549723009	hypothetical protein	PAAR
33	STMDT2_02871	336613..336876 [+], 264	549723010	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

EvpC , STM0277, EvpC, STY2606, ROD_34191

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	STMDT2_02721(sciK)	316867..317352 [+], 486	549722994	virulence associated protein	EvpC
2	STMDT2_02731	317657..318142 [+], 486	549722995	hypothetical protein	STM0277
3	STMDT2_02751(sciK1)	318653..319138 [+], 486	549722997	virulence associated protein	EvpC
4	STMDT2_23441	2477516..2477884 [+], 369	549725031	hypothetical protein	STY2606
5	STMDT2_30251	3248713..3249198 [-], 486	549725694	hypothetical protein	ROD_34191

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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	STMDT2_02741	318127..318510 [+], 384	549722996	hypothetical protein	STM0278
2	STMDT2_23451	2477884..2478402 [+], 519	549725032	putative lipoprotein	STY2607

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Proteins        Genes

N/A