SecReT6
I. Summary
SecReT6 ID43 experimental
StrainVibrio parahaemolyticus RIMD 2210633
Repliconchromosome I [Browse all T6SS(s) in this replicon]
AccessionNC_004603
Location1486402..1526996
CommentAdhesion to cultured cell monolayers; V. parahaemolyticus T6SS1 effectors mediate its antibacterial activity
Functionanti-eukaryotic and anti-bacterial;effector translocation;adherence;virulence
T6SS TypeType i; subtype i1
experimental Experimental investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111121111
ComponentTssGTssJTssKTssM
Number1111
14
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1VP13881483439..1485205 [+], 176728898162hypothetical protein  VP1388 (e)
2VP13891485278..1486405 [+], 112828898163hypothetical protein  VP1389 (i)
3VP13901486402..1491144 [+], 474328898164hypothetical protein  TagL
4VP13911491226..1492857 [-], 163228898165transcriptional regulator 
5VP13921492844..1495516 [-], 267328898166ClpA/B-type protease  TssH
6VP13931495971..1496489 [+], 51928898167BfdA protein  TssD
7VP13941496562..1498640 [+], 207928898168VgrG protein  TssI
8VP13951498640..1499125 [+], 48628898169hypothetical protein 
9VP13961499195..1499968 [+], 77428898170hypothetical protein 
10VP13971499937..1500536 [+], 60028898171hypothetical protein 
11VP13981500517..1501509 [+], 99328898172hypothetical protein 
12VP13991501502..1502446 [+], 94528898173hypothetical protein 
13VP14001502624..1504684 [+], 206128898174hypothetical protein 
14VP14011504684..1506258 [+], 157528898175hypothetical protein  TssA
15VP14021506285..1506791 [+], 50728898176hypothetical protein  TssB
16VP14031506800..1508275 [+], 147628898177hypothetical protein  TssC
17VP14041508283..1508747 [+], 46528898178hypothetical protein  TssE
18VP14051508758..1510506 [+], 174928898179hypothetical protein  TssF
19VP14061510470..1511501 [+], 103228898180hypothetical protein  TssG
20VP14071511565..1512017 [-], 45328898181transcriptional regulator 
21VP14081512050..1515439 [-], 339028898182IcmF-like protein  TssM
22VP14091515461..1516771 [-], 131128898183hypothetical protein  TssA
23VP14101517264..1517875 [+], 61228898184hypothetical protein 
24VP14111517885..1519399 [+], 151528898185hypothetical protein  Fha
25VP14121519392..1519892 [+], 50128898186hypothetical protein  TssJ
26VP14131519904..1521229 [+], 132628898187hypothetical protein  TssK
27VP14141521211..1522017 [+], 80728898188hypothetical protein  TssL
28VP14151522119..1524323 [+], 220528898189hypothetical protein  VP1415 (e)
29VP14161524323..1524916 [+], 59428898190hypothetical protein  VP1416 (i)
30VP14171524886..1525467 [+], 58228898191hypothetical protein 
31VP14181525615..1526049 [+], 43528898192hypothetical protein 
32VP14191526430..1526996 [+], 56728898193hypothetical protein 
33VP14201527018..1527506 [+], 48928898194hypothetical protein 
34VP14211527691..1527984 [+], 29428898195hypothetical protein 
35VP14221528144..1528746 [+], 60328898196SM-20-like protein 
36VP14231528811..1530076 [-], 126628898197hypothetical protein 
37VP14241530281..1530430 [-], 15028898198hypothetical protein 
38VP14251530652..1531842 [+], 119128898199alcohol dehydrogenase 
 
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
VP1388 , VP1393, VP1415, VPA1263

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1VP13881483439..1485205 [+], 176728898162hypothetical protein VP1388
2VP13931495971..1496489 [+], 51928898167BfdA protein VP1393
3VP14151522119..1524323 [+], 220528898189hypothetical protein VP1415
4VPA12631341842..1344451 [+], 261028901118hypothetical protein VPA1263
Data from experimental literature

Download FASTA format files
Proteins        Genes

Homology Immunity protein list
VP1389, VP1416   Vti2

Immunity protein identified
#Locus tag(Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1VP13891485278..1486405 [+], 112828898163hypothetical protein VP1389
2VP14161524323..1524916 [+], 59428898190hypothetical protein VP1416
Data from experimental literature

Download FASTA format files
Proteins        Genes
Regulatory element identified
OpaR
RegulatorDescriptionReference
OpaR (VP2516)RepressorPMID: 23613791

VP1391
RegulatorDescriptionReference
VP1391ActivatorPMID: 23613791

VP1407
RegulatorDescriptionReference
VP1407ActivatorPMID: 23613791

H-NS
RegulatorDescriptionReference
H-NS (VP1133)RepressorPMID: 24987102

The information on regulator interaction.

#homolog effector locus tagRegulator wayFunctionRegulate targetDescription
1vp2049 (Thymidylate kinase,Tmk) Unknown+T6SS1 (VgrG1) expression and secretionTmk,or one of the downstream products of its enzymatic activity, is critical for activating T6SS1.
2VP1028 (TfoY)c-di-GMP +T6SS1 (VgrG1) expression and secretionTfoY is a positive regulator required and sufficient for T6SS1 activation.
3vp1391Unknown+T6SS1 (VgrG1) expression and secretionTfoY-mediated activation of T6SS1 was dependent on the presence of both vp1391 and vp1407.
4vp1407Unknown+T6SS1 (VgrG1) expression and secretionTfoY-mediated activation of T6SS1 was dependent on the presence of both vp1391 and vp1407.
5VP2516 (opaR)-vp1407OpaR was previously suggested to directly bind to promoter regions of V. parahaemolyticus T6SS1 operons, including the pro- moter of the operon encoding the positive downstream reg- ulator, VP1407.
6VP1133 (hns)Transcriptional-VP1028 (TfoY).
7VP2762 (AphA)Transcription regulator-T6SS1 transcriptAphA appears to negatively regulate the transcription of T6SS2 in an indirect manner.
8VP2516 (opaR)Transcription regulator-VP1388 promotorOpaR represses the transcription of VP1388-1390, VP1400-1406, and VP1409-1407 in a direct manner.
9VP2516 (opaR)VP1400 promotor.
10VP2516 (opaR)VP1409 promotor.
11VP0820 (ToxR)Transcription regulator-VP1400 promotorToxR represses the transcription of VP1400-1406 and VP1409-1407 in a direct manner.
12VP0820 (ToxR)VP1409 promotor.
13VPA1088 (cdpA)c-di-GMP-VP1028 (TfoY)A phosphodiesterase keeps c-di-GMP in low levels.
14VPA0739 (vdcA)c-di-GMP+VP1028 (TfoY)c-di-GMP-producing diguanylate cyclase.
15VP2516 (OpaR)Transcription regulator+T6SS1TfoX-mediated T6SS induction in V. parahaemolyticus requires co-regulation by OpaR.
16VP1028 (TfoY)c-di-GMP+T6SS1TfoY solely led to T6SS1-mediated prey killing .
(1) Salomon D et al. (2014). H-NS regulates the Vibrio parahaemolyticus type VI secretion system 1. Microbiology. 160(Pt 9):1867-73. [PudMed:24987102] experimental
(2) Salomon D et al. (2014). Marker for type VI secretion system effectors. Proc Natl Acad Sci U S A. 111(25):9271-6. [PudMed:24927539] experimental in_silico
(3) Salomon D et al. (2013). Vibrio parahaemolyticus Type VI Secretion System 1 Is Activated in Marine Conditions to Target Bacteria, and Is Differentially Regulated from System 2. PLoS One. 8(4):e61086. [PudMed:23613791] experimental
(4) Ma L et al. (2012). Expression of the Type VI Secretion System 1 Component Hcp1 Is Indirectly Repressed by OpaR in Vibrio parahaemolyticus. Scientific World Journal. 2012:982140. [PudMed:22924031] experimental
(5) Yu Y et al. (2012). Putative type VI secretion systems of Vibrio parahaemolyticus contribute to adhesion to cultured cell monolayers. Arch Microbiol. 194(10):827-35. [PudMed:22535222] experimental
(6) Boyer F et al. (2009). Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources. BMC Genomics. 10:104. [PudMed:19284603] in_silico
 
experimental This literature contains experimental investigation
in_silico This literature contains bioinformatics investigation

Genomics & Bioinformatics Group in MML, SJTU