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_3547	3902173..3905079 [+], 2907	170025762	ATP-dependent helicase HepA
2	YPK_3548	3905041..3905187 [-], 147	170025763	hypothetical protein
3	YPK_3549	3905334..3905687 [-], 354	170025764	hypothetical protein
4	YPK_3550	3905709..3909203 [-], 3495	170025765	type VI secretion protein IcmF	TssM
5	YPK_3551	3909212..3910822 [-], 1611	170025766	hypothetical protein	TssL
6	YPK_3552	3910819..3912174 [-], 1356	170025767	type VI secretion protein	TssK
7	YPK_3553	3912294..3912785 [-], 492	170025768	putative lipoprotein	TssJ
8	YPK_3554	3912778..3913143 [-], 366	170025769	hypothetical protein	PAAR
9	YPK_3555	3913149..3913766 [-], 618	170025770	hypothetical protein
10	YPK_3556	3913759..3914862 [-], 1104	170025771	pentapeptide repeat-containing protein
11	YPK_3557	3914888..3917107 [-], 2220	170025772	pentapeptide repeat-containing protein
12	YPK_3558	3917120..3919468 [-], 2349	170025773	ImpA family type VI secretion-associated protein	TssI
13	YPK_3559	3919572..3922160 [-], 2589	170025774	type VI secretion ATPase	TssH
14	YPK_3560	3922178..3923161 [-], 984	170025775	type VI secretion protein	TssG
15	YPK_3561	3923154..3924998 [-], 1845	170025776	type VI secretion protein	TssF
16	YPK_3562	3925031..3925474 [-], 444	170025777	type VI secretion system lysozyme-like protein	TssE
17	YPK_3563	3925548..3926066 [-], 519	170025778	hypothetical protein	TssD
18	YPK_3564	3926229..3927740 [-], 1512	170025779	EvpB family type VI secretion protein	TssC
19	YPK_3565	3927740..3928300 [-], 561	170025780	type VI secretion protein	TssB
20	YPK_3566	3928311..3929297 [-], 987	170025781	ImpA domain-containing protein	TssA
21	YPK_3567	3929654..3930397 [+], 744	170025782	hypothetical protein
22	YPK_3568	3931620..3932240 [+], 621	170025783	pseudouridine synthase
23	YPK_3569 (djlA)	3932557..3933390 [-], 834	170025784	Dna-J like membrane chaperone 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

Ypk_3549 , YPK_3558, YPK_3563

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	YPK_3549	3905334..3905687 [-], 354	170025764	hypothetical protein	Ypk_3549
2	YPK_3558	3917120..3919468 [-], 2349	170025773	ImpA family type VI secretion-associated protein	YPK_3558
3	YPK_3563	3925548..3926066 [-], 519	170025778	hypothetical protein	YPK_3563
Data from experimental literature

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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