I. Summary
SecReT6 ID2 insolico
StrainVibrio cholerae O1 biovar El Tor str. N16961
Repliconchromosome II (Vas) [Browse all T6SS(s) in this replicon]
CommentCytotoxicity towards Dictyostelium and cultured mammalian macrophages; inflammatory response, diarrhoea and actin cross-linking in mouse intestine; Killing of E. coli, Salmonella and Citrobacter rodentium
T6SS TypeType i; subtype i1
insolico Bioinformatics 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
1VCA0099106851..107891 [+], 104115600870Gfo/Idh/MocA family oxidoreductase 
2VCA0100107928..108299 [-], 37215600871phage shock protein E 
3VCA0101108299..109855 [-], 155715600872hypothetical protein 
4VCA0102110031..110690 [-], 66015600873CbbY family protein 
5VCA0103110871..112649 [+], 177915600874sulfate permease 
6VCA0104112691..113356 [-], 66615600875ribosomal large subunit pseudouridine synthase A 
7VCA0105115142..115426 [+], 28515600876hypothetical protein  PAAR
8VCA0106115341..116414 [+], 107415600877hypothetical protein 
9VCA0107116846..117352 [+], 50715600878hypothetical protein  TssB
10VCA0108117393..118871 [+], 147915600879hypothetical protein  TssC
11VCA0109118874..119311 [+], 43815600880hypothetical protein  TssE
12VCA0110119317..121086 [+], 177015600881hypothetical protein  TssF
13VCA0111121050..122066 [+], 101715600882hypothetical protein  TssG
14VCA0112122069..123556 [+], 148815600883hypothetical protein  Fha
15VCA0113123559..124035 [+], 47715600884hypothetical protein  TssJ
16VCA0114124042..125376 [+], 133515600885hypothetical protein  TssK
17VCA0115125379..126152 [+], 77415600886hypothetical protein  TssL
18VCA0116126178..128787 [+], 261015600887clpB protein  TssH
19VCA0117128790..130382 [+], 159315600888sigma-54 dependent transcriptional regulator  VasH
20VCA0118130352..131035 [+], 68415600889hypothetical protein  VCA0118
21VCA0119131045..132454 [+], 141015600890hypothetical protein  TssA
22VCA0120132470..136015 [+], 354615600891IcmF-related protein  TssM
23VCA0121136063..137328 [+], 126615600892hypothetical protein  TssA
24VCA0122137379..137621 [+], 24315600893hypothetical protein 
25VCA0123137581..140634 [+], 305415600894vgrG protein  TssI
26VCA0124140631..140999 [+], 36915600895hypothetical protein  TsiV3 (i)
27VCA0125141147..141407 [-], 26115600896hypothetical protein 
28VCA0126141382..141591 [+], 21015600897hypothetical protein 
29VCA0127141691..142110 [+], 420229220825D-ribose pyranase 
30VCA0128142137..143639 [+], 150315600899D-ribose transporter ATP binding protein 
31VCA0129 (rbsC)143636..144634 [+], 99915600900ribose ABC transporter permease 
32VCA0130144693..145577 [+], 88515600901D-ribose transporter subunit RbsB 
33VCA0131145716..146636 [+], 92115600902ribokinase 
34VCA0132146647..147651 [+], 100515600903ribose operon repressor 
35VCA0134148508..149239 [+], 73215600904uridine phosphorylase 
36VCA0135149379..150059 [+], 68115600905cyclic nucleotide binding protein 
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

Download FASTA format files
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
VCA0017 , VCA0018, VCA0020 (VasX), VCA0118, VCA0123, VCA0285, VC1415, VC1416, VC1418 (TseL, Tle2)

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1VCA001719781..20299 [+], 51915600788hcp protein VCA0017
2VCA001820427..22511 [+], 208515600789vgrG protein VCA0018
3VCA002023395..26652 [+], 325815600791hypothetical protein (VasX)VCA0020 (VasX)
4VCA0118130352..131035 [+], 68415600889hypothetical protein VCA0118
5VCA0123137581..140634 [+], 305415600894vgrG protein VCA0123
6VCA0285305200..305871 [+], 67215601051hypothetical protein VCA0285
7VC14151509632..1510150 [+], 51915641426hcp protein VC1415
8VC14161510278..1513769 [+], 349215641427vgrG protein VC1416
9VC14181514611..1516536 [+], 192615641429hypothetical protein (TseL, Tle2)VC1418 (TseL, Tle2)
Data from experimental literature

Download FASTA format files
Proteins        Genes

Homology Immunity protein list
VCA0021 (TsiV2), VCA0124 (TsiV3), VCA0286, VC1419 (TsiV1)

Immunity protein identified
#Locus tag(Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1VCA002126653..27381 [+], 72915600792hypothetical protein (TsiV2)VCA0021 (TsiV2)
2VCA0124140631..140999 [+], 36915600895hypothetical protein (TsiV3)VCA0124 (TsiV3)
3VCA0286305873..306223 [+], 35115601052hypothetical protein VCA0286
4VC14191516533..1517276 [+], 74415641430hypothetical protein (TsiV1)VC1419 (TsiV1)
Data from experimental literature

Download FASTA format files
Proteins        Genes
Regulatory element identified
VasH (VCA0117)ActivatorPMID: 21949076

HapRActivatorPMID: 19701456

LuxQ (VCA0736)Can be activator or repressorPMID: 19701456

OscR (VCA0029)RepressorPMID: 22083711

VCA0122ActivatorPMID: 21909372

HlyU (VC0678)ActivatorPMID: 8557353

Hfq (VC0347)RepressorPMID: 19701456

DksA (VC0596)Indirect activatorPMID: 19329638

TsrA (VC0070)RepressorPMID: 21084635

LuxO (VC1021)Repressor: HapRPMID: 21084635

CqsA (VCA0523)ActivatorPMID: 19701456

LuxS (VC0557)ActivatorPMID: 19701456

Qrr sRNAs
Qrr sRNAsRepressorPMID: 24698180

RpoN (VC2529)Activator: Hcp operons and VgrG-3PMID: 22723378

TfoXActivatorPMID: 25554784

QstRActivatorPMID: 25554784

thioureaRepressorPMID: 25646446

VxrB (VCA0566)ActivatorPMID: 26000450

Adaptors list
VC1417(NC_002505, Vibrio cholerae O1 biovar El Tor str. N16961 chromosome II (Vas) T6SS secreted)
(1) Altindis E et al. (2015). Secretome Analysis of Vibrio cholerae Type VI Secretion System Reveals a New Effector-Immunity Pair. MBio. pii: e00075-15. [PudMed:25759499] experimental
(2) Borgeaud S et al. (2015). Bacterial evolution. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science. 347(6217):63-7. [PudMed:25554784] experimental
(3) Jeong JH et al. (2014). Purification, crystallization and preliminary X-ray crystallographic analysis of TssL from Vibrio cholerae. Acta Crystallogr F Struct Biol Commun. 70(Pt 9):1260-3. [PudMed:25195905] experimental in_silico
(4) Yang X et al. (2014). Molecular mechanism for self-protection against the type VI secretion system in Vibrio cholerae. Acta Crystallogr D Biol Crystallogr. 70(Pt 4):1094-103. [PudMed:24699653] experimental in_silico
(5) Shao Y et al. (2014). Quorum regulatory small RNAs repress type VI secretion in Vibrio cholerae. Mol Microbiol. 92(5):921-30. [PudMed:24698180] experimental
(6) Miyata ST et al. (2013). Dual Expression Profile of Type VI Secretion System Immunity Genes Protects Pandemic Vibrio cholerae. PLoS Pathog. 9(12):e1003752. [PudMed:24348240] experimental
(7) Broms JE et al. (2013). A functional VipA-VipB interaction is required for the type VI secretion system activity of Vibrio cholerae O1 strain A1552. BMC Microbiol. 13(1):96. [PudMed:23642157] experimental
(8) Russell AB et al. (2013). Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature. 496(7446):508-12. [PudMed:23552891] experimental
(9) Dong TG et al. (2013). Identification of T6SS-dependent effector and immunity proteins by Tn-seq in Vibrio cholerae. Proc Natl Acad Sci U S A . 110(7):2623-8. [PudMed:23362380] experimental
(10) Unterweger D et al. (2012). Constitutive type VI secretion system expression gives Vibrio cholerae intra- and interspecific competitive advantages. PLoS One. 7(10):e48320. [PudMed:23110230] experimental
(11) Dong TG et al. (2012). Characterization of the RpoN regulon reveals differential regulation of T6SS and new flagellar operons in Vibrio cholerae O37 strain V52. Nucleic Acids Res. 40(16):7766-75. [PudMed:22723378] experimental
(12) Basler M et al. (2012). Type VI secretion requires a dynamic contractile phage tail-like structure. Nature. 483(7388):182-6. [PudMed:22367545]
(13) Ishikawa T et al. (2012). Pathoadaptive conditional regulation of the type VI secretion system in Vibrio cholerae O1 strains. Infect Immun. 80(2):575-84. [PudMed:22083711] experimental
(14) Kitaoka M et al. (2011). VasH is a transcriptional regulator of the type VI secretion system functional in endemic and pandemic Vibrio cholerae. J Bacteriol. 193(23):6471-82. [PudMed:21949076]
(15) Zheng J et al. (2011). Genetic analysis of anti-amoebae and anti-bacterial activities of the type VI secretion system in Vibrio cholerae. PLoS One. 6(8):e23876. [PudMed:21909372] experimental
(16) Pietrosiuk A et al. (2011). Molecular basis for the unique role of the AAA+ chaperone ClpV in type VI protein secretion. J Biol Chem. 286(34):30010-21. [PudMed:21733841] experimental
(17) Miyata ST et al. (2011). Vibrio cholerae requires the type VI secretion system virulence factor VasX to kill Dictyostelium discoideum. Infect Immun. 79(7):2941-9. [PudMed:21555399] experimental
(18) Records AR (2011). The type VI secretion system: a multipurpose delivery system with a phage-like machinery. Mol Plant Microbe Interact. 24(7):751-7. [PudMed:21361789] in_silico
(19) Kitaoka M et al. (2011). Antibiotic resistance mechanisms of Vibrio cholerae. J Med Microbiol. 60(Pt 4):397-407. [PudMed:21252269]
(20) MacIntyre DL et al. (2010). The Vibrio cholerae type VI secretion system displays antimicrobial properties. Proc Natl Acad Sci U S A. 107(45):19520-4. [PudMed:20974937] experimental
(21) Ma AT et al. (2009). Translocation of a Vibrio cholerae type VI secretion effector requires bacterial endocytosis by host cells. Cell Host Microbe. 5(3):234-43. [PudMed:19286133] experimental
(22) Pukatzki S et al. (2007). Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci U S A. 104(39):15508-13. [PudMed:17873062] experimental
(23) Pukatzki S et al. (2006). Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc Natl Acad Sci U S A. 103(5):1528-33. [PudMed:16432199] experimental
experimental This literature contains experimental investigation
in_silico This literature contains bioinformatics investigation