I. Summary

SecReT6 ID	822
Strain	Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_021814
Location	3234804..3262201
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	CFSAN001921_15945	3229964..3230227 [-], 264	525841087	hypothetical protein
2	CFSAN001921_15950	3230221..3234315 [-], 4095	525841088	type IV secretion protein Rhs	PAAR
3	CFSAN001921_15955	3234334..3234780 [-], 447	525839266	hypothetical protein
4	CFSAN001921_15960	3234804..3236993 [-], 2190	525839267	type VI secretion protein Vgr	TssI
5	CFSAN001921_15965	3237390..3237908 [-], 519	525841089	SPI-6 associated protein
6	CFSAN001921_15970	3237935..3238321 [-], 387	525841090	hypothetical protein
7	CFSAN001921_15975	3238348..3239136 [-], 789	525839268	hypothetical protein
8	CFSAN001921_15980	3239136..3243005 [-], 3870	525839269	membrane protein	TssM
9	CFSAN001921_15985	3243039..3243482 [-], 444	525839270	Shiga toxin A subunit
10	CFSAN001921_15990	3243673..3244446 [-], 774	525841091	membrane protein
11	CFSAN001921_15995	3244451..3245755 [-], 1305	525839271	membrane protein	TssL
12	CFSAN001921_16000	3245752..3247095 [-], 1344	525839272	type VI secretion protein	TssK
13	CFSAN001921_16005	3247099..3247635 [-], 537	525839273	outer membrane lipoprotein	TssJ
14	CFSAN001921_16010	3247702..3248187 [-], 486	525839274	Hcp1 family type VI secretion system effector	TssD
15	CFSAN001921_16015	3248330..3248713 [-], 384	525839275	hypothetical protein	STM0278 (i)
16	CFSAN001921_16020	3248698..3249183 [-], 486	525839276	hypothetical protein	STM0277 (e)
17	CFSAN001921_16025	3249488..3249973 [-], 486	525839277	Hcp1 family type VI secretion system effector	TssD
18	CFSAN001921_16030	3250859..3252367 [-], 1509	525839278	EvpB family type VI secretion protein	TssC
19	CFSAN001921_16035	3252391..3252933 [-], 543	525839279	type VI secretion protein	TssB
20	CFSAN001921_16040	3253033..3255672 [-], 2640	525839280	protein disaggregation chaperone	TssH
21	CFSAN001921_16045	3256040..3256942 [+], 903	525839281	hypothetical protein
22	CFSAN001921_16050	3256929..3257753 [+], 825	525839282	hypothetical protein	TagJ
23	CFSAN001921_16055	3257750..3258244 [+], 495	525839283	cytoplasmic protein	TssE
24	CFSAN001921_16060	3258260..3260143 [+], 1884	525841092	type VI secretion protein	TssF
25	CFSAN001921_16065	3260140..3261135 [+], 996	525839284	SPI-6 associated protein	TssG
26	CFSAN001921_16070	3261146..3262201 [+], 1056	525839285	hypothetical protein	TssA
27	CFSAN001921_16080	3262733..3263473 [-], 741	525839286	DNA polymerase III subunit epsilon
28	CFSAN001921_16085	3263528..3263995 [+], 468	525839287	ribonuclease H
29	CFSAN001921_16090	3263992..3264714 [-], 723	525839288	hypothetical protein
30	CFSAN001921_16095	3264749..3265504 [+], 756	525839289	hydroxyacylglutathione hydrolase
31	CFSAN001921_16100 (mltD)	3265576..3266943 [+], 1368	525839290	membrane 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

ROD_34191 , EvpC, STM0277, EvpC, STY2606

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	CFSAN001921_01365	275988..276473 [+], 486	525837011	hypothetical protein	ROD_34191
2	CFSAN001921_16010	3247702..3248187 [-], 486	525839274	Hcp1 family type VI secretion system effector	EvpC
3	CFSAN001921_16020	3248698..3249183 [-], 486	525839276	hypothetical protein	STM0277
4	CFSAN001921_16025	3249488..3249973 [-], 486	525839277	Hcp1 family type VI secretion system effector	EvpC
5	CFSAN001921_04910	1028787..1029155 [-], 369	525840654	hypothetical protein	STY2606

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Proteins        Genes

Homology Immunity protein list

STY2607, STM0278

Immunity protein identified
#	Locus tag(Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	CFSAN001921_04905	1028269..1028787 [-], 519	525837536	hypothetical protein	STY2607
2	CFSAN001921_16015	3248330..3248713 [-], 384	525839275	hypothetical protein	STM0278

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Proteins        Genes

N/A