I. Summary

SecReT6 ID	260
Strain	Yersinia pseudotuberculosis YPIII
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_010465
Location	3905709..3929297
Comment	An function in H(+) extrusion under acid conditions for acid resistance
Function	effector translocation
T6SS Type	Type i; subtype i3
Experimental investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	1	1	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	YPK_RS17830 (rapA)	3902173..3905079 [+], 2907	499505079	RNA polymerase-associated protein RapA
2	YPK_RS17835	3905334..3905687 [-], 354	488139260	hypothetical protein
3	YPK_RS17840 (tssM)	3905709..3909150 [-], 3442	pseudogene	type VI secretion system membrane subunit TssM
4	YPK_RS17845	3909212..3910822 [-], 1611	501261573	type IVB secretion system protein IcmH/DotU
5	YPK_RS17850 (tssK)	3910819..3912174 [-], 1356	488139262	type VI secretion system baseplate subunit TssK
6	YPK_RS17855 (tssJ)	3912294..3912785 [-], 492	501261574	type VI secretion system lipoprotein TssJ
7	YPK_RS17860	3912778..3913143 [-], 366	488143529	DUF4150 domain-containing protein
8	YPK_RS17865	3913149..3913766 [-], 618	488139265	DUF3540 domain-containing protein
9	YPK_RS17870	3913759..3914862 [-], 1104	488143531	pentapeptide repeat-containing protein
10	YPK_RS17875	3914888..3917107 [-], 2220	488152879	pentapeptide repeat-containing protein
11	YPK_RS17880 (vgrG)	3917120..3919468 [-], 2349	499505075	type VI secretion system tip protein VgrG
12	YPK_RS17885 (tssH)	3919572..3922160 [-], 2589	488139267	type VI secretion system ATPase TssH
13	YPK_RS17890 (tssG)	3922178..3923161 [-], 984	501261575	type VI secretion system baseplate subunit TssG
14	YPK_RS17895 (tssF)	3923154..3924998 [-], 1845	501261576	type VI secretion system baseplate subunit TssF
15	YPK_RS17900	3925031..3925474 [-], 444	488139270	type VI secretion system baseplate subunit TssE
16	YPK_RS17905	3925548..3926066 [-], 519	501261577	type VI secretion system tube protein Hcp
17	YPK_RS17910 (tssC)	3926229..3927731 [-], 1503	488139272	type VI secretion system contractile sheath large subunit
18	YPK_RS17915 (tssB)	3927740..3928300 [-], 561	488139273	type VI secretion system contractile sheath small subunit
19	YPK_RS17920	3928311..3929324 [-], 1014	488139274	ImpA family type VI secretion system protein
20	YPK_RS17925	3929654..3930397 [+], 744	488143539	hexameric transcriptional regulator RovC
21	YPK_RS17930 (rluA)	3931620..3932240 [+], 621	488139277	bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA
22	YPK_RS17935 (djlA)	3932557..3933390 [-], 834	501261578	co-chaperone DjlA

 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

Ypk_3549 , YPK_3558, YPK_3563

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog

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Proteins        Genes

N/A

Regulatory element identified

YpsI

Regulator	Description	Reference
YpsI (YPK_1656)	Activator	PMID: 21298257

OmpR

Regulator	Description	Reference
OmpR (YPK_0172)	Activator	PMID: 23094603

YtbI

Regulator	Description	Reference
YtbI (YPK_0792)	Activator	PMID: 21298257

The information on regulator interaction.

#	homolog effector locus tag	Regulator way	Function	Regulate target	Description
1	YPK_4079 (OxyR)	Transcription regulator	+	T6SS-4 promoter region	OxyR specifically recognizes an operator within the T6SS-4 promoter,and specifically activates the expression of T6SS-4.
2	ypk_3425 (RpoS)	Transcription regulator	+	unknown	RpoS positively regulates T6SS4 expre-ssion by directly binding to the T6SS4 promoter.
3	YPK_3449 (RelA)	(p)ppGpp	+	YPK_1551 (RovM)	The (p)ppGpp synthase RelA functions upstream of RovM and RovA to regulate T6SS4 expression.
4	YPK_3449 (RelA)			YPK_1876 (RovA)	.
5	YPK_1876 (RovA)	(p)ppGpp	+	T6SS-4 promoter region	RovA positively regulates T6SS4 expression by recognizing two conserved AT-rich RovA-binding sites in the T6SS4 promoter.
6	YPK_1876 (RovA)			T6SS-4 promoter region	.
7	YPK_1551 (RovM)	(p)ppGpp	+	T6SS-4 promoter region	RovM upregulates T6SS4 by binding directly to the T6SS4 promoter, even also suppressing the expression of RovA.

(1) Wang T et al. (2015). Type VI Secretion System Transports Zn2+ to Combat Multiple Stresses and Host Immunity. PLoS Pathog. 11(7):e1005020. [PudMed:26134274]

(2) Zhang W et al. (2012). A type VI secretion system regulated by OmpR in Yersinia pseudotuberculosis functions to maintain intracellular pH homeostasis. Environ Microbiol. 15(2):557-69. [PudMed:23094603]

(3) Zhang W et al. (2011). Modulation of a thermoregulated type VI secretion system by AHL-dependent quorum sensing in Yersinia pseudotuberculosis. Arch Microbiol. 193(5):351-63. [PudMed:21298257]

This literature contains experimental investigation