I. Summary
SecReT6 ID260 experimental
StrainYersinia pseudotuberculosis YPIII
Repliconchromosome [Browse all T6SS(s) in this replicon]
CommentAn function in H(+) extrusion under acid conditions for acid resistance
Functioneffector translocation
T6SS TypeType i; subtype i3
experimental Experimental investigation has been performed on this T6SS.

II. T6SS components
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1YPK_RS17830 (rapA)3902173..3905079 [+], 2907499505079RNA polymerase-associated protein RapA 
2YPK_RS178353905334..3905687 [-], 354488139260hypothetical protein 
3YPK_RS17840 (tssM)3905709..3909150 [-], 3442pseudogenetype VI secretion system membrane subunit TssM 
4YPK_RS178453909212..3910822 [-], 1611501261573type IVB secretion system protein IcmH/DotU 
5YPK_RS17850 (tssK)3910819..3912174 [-], 1356488139262type VI secretion system baseplate subunit TssK 
6YPK_RS17855 (tssJ)3912294..3912785 [-], 492501261574type VI secretion system lipoprotein TssJ 
7YPK_RS178603912778..3913143 [-], 366488143529DUF4150 domain-containing protein 
8YPK_RS178653913149..3913766 [-], 618488139265DUF3540 domain-containing protein 
9YPK_RS178703913759..3914862 [-], 1104488143531pentapeptide repeat-containing protein 
10YPK_RS178753914888..3917107 [-], 2220488152879pentapeptide repeat-containing protein 
11YPK_RS17880 (vgrG)3917120..3919468 [-], 2349499505075type VI secretion system tip protein VgrG 
12YPK_RS17885 (tssH)3919572..3922160 [-], 2589488139267type VI secretion system ATPase TssH 
13YPK_RS17890 (tssG)3922178..3923161 [-], 984501261575type VI secretion system baseplate subunit TssG 
14YPK_RS17895 (tssF)3923154..3924998 [-], 1845501261576type VI secretion system baseplate subunit TssF 
15YPK_RS179003925031..3925474 [-], 444488139270type VI secretion system baseplate subunit TssE 
16YPK_RS179053925548..3926066 [-], 519501261577type VI secretion system tube protein Hcp 
17YPK_RS17910 (tssC)3926229..3927731 [-], 1503488139272type VI secretion system contractile sheath large subunit 
18YPK_RS17915 (tssB)3927740..3928300 [-], 561488139273type VI secretion system contractile sheath small subunit 
19YPK_RS179203928311..3929324 [-], 1014488139274ImpA family type VI secretion system protein 
20YPK_RS179253929654..3930397 [+], 744488143539hexameric transcriptional regulator RovC 
21YPK_RS17930 (rluA)3931620..3932240 [+], 621488139277bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA 
22YPK_RS17935 (djlA)3932557..3933390 [-], 834501261578co-chaperone DjlA 
flank 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.

2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.

3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.

Homology Effector list
Ypk_3549 , YPK_3558, YPK_3563

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

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Proteins        Genes
Regulatory element identified
YpsI (YPK_1656)ActivatorPMID: 21298257

OmpR (YPK_0172)ActivatorPMID: 23094603

YtbI (YPK_0792)ActivatorPMID: 21298257

The information on regulator interaction.

#homolog effector locus tagRegulator wayFunctionRegulate targetDescription
1YPK_4079 (OxyR)Transcription regulator+T6SS-4 promoter regionOxyR specifically recognizes an operator within the T6SS-4 promoter,and specifically activates the expression of T6SS-4.
2ypk_3425 (RpoS)Transcription regulator+unknownRpoS positively regulates T6SS4 expre-ssion by directly binding to the T6SS4 promoter.
3YPK_3449 (RelA)(p)ppGpp+YPK_1551 (RovM)The (p)ppGpp synthase RelA functions upstream of RovM and RovA to regulate T6SS4 expression.
4YPK_3449 (RelA)YPK_1876 (RovA).
5YPK_1876 (RovA)(p)ppGpp+T6SS-4 promoter regionRovA positively regulates T6SS4 expression by recognizing two conserved AT-rich RovA-binding sites in the T6SS4 promoter.
6YPK_1876 (RovA)T6SS-4 promoter region.
7YPK_1551 (RovM)(p)ppGpp+T6SS-4 promoter regionRovM 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] experimental
(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] experimental
(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]
experimental This literature contains experimental investigation