SecReT6
I. Summary
SecReT6 ID41 insolico
StrainPseudomonas syringae pv. tomato str. DC3000
Repliconchromosome [Browse all T6SS(s) in this replicon]
AccessionNC_004578
Location2796816..2829435
Comment
FunctionN/A
T6SS TypeType i; subtype i1
insolico Bioinformatics investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111101111
ComponentTssGTssJTssKTssM
Number1111
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1PSPTO_RS131002792008..2792712 [-], 705764496382DUF1275 domain-containing protein 
2PSPTO_RS131052792754..2792981 [-], 228489478362hypothetical protein 
3PSPTO_RS131102793112..2793453 [-], 342494456855FKBP-type peptidyl-prolyl cis-trans isomerase 
4PSPTO_RS131152793591..2793875 [-], 285499416599hypothetical protein 
5PSPTO_RS131202794541..2796109 [+], 1569499416600TerC family protein 
6PSPTO_RS131252796179..2796754 [-], 576499416601GNAT family N-acetyltransferase 
7PSPTO_RS131302796816..2797496 [-], 681499416602hypothetical protein 
8PSPTO_RS131352797493..2800891 [-], 33991818936131hypothetical protein 
9PSPTO_RS131402800881..2801763 [-], 883pseudogeneDUF4123 domain-containing protein 
10PSPTO_RS131452801756..2803798 [-], 2043499416606type VI secretion system tip protein VgrG 
11PSPTO_RS131502803874..2804389 [-], 516494457196Hcp family type VI secretion system effector 
12PSPTO_RS13155 (tssA)2804890..2805867 [+], 978pseudogenetype VI secretion system protein TssA 
13PSPTO_RS131602806011..2806988 [-], 978494457842IS5-like element ISPssy family transposase 
14PSPTO_RS131652807051..2807629 [+], 579pseudogenetype VI secretion system domain-containing protein 
15PSPTO_RS13170 (tssB)2807665..2808165 [+], 501499416607type VI secretion system contractile sheath small subunit 
16PSPTO_RS13175 (tssC)2808195..2809670 [+], 1476499416608type VI secretion system contractile sheath large subunit 
17PSPTO_RS13180 (tssE)2809686..2810093 [+], 408499416609type VI secretion system baseplate subunit TssE 
18PSPTO_RS13185 (tssF)2810191..2811978 [+], 1788499416610type VI secretion system baseplate subunit TssF 
19PSPTO_RS13190 (tssG)2811942..2812949 [+], 1008499416611type VI secretion system baseplate subunit TssG 
20PSPTO_RS13195 (tssH)2812959..2815562 [+], 2604499416612type VI secretion system ATPase TssH 
21PSPTO_RS132002815564..2817093 [+], 1530499416613sigma-54-dependent Fis family transcriptional regulator 
22PSPTO_RS13205 (tssJ)2817337..2817828 [+], 492494457187type VI secretion system lipoprotein TssJ 
23PSPTO_RS13210 (tssK)2817825..2819156 [+], 1332497899618type VI secretion system baseplate subunit TssK 
24PSPTO_RS132152819138..2820028 [+], 891815830606type IVB secretion system protein IcmH/DotU 
25PSPTO_RS13220 (tssM)2820042..2823548 [+], 3507499416615type VI secretion system membrane subunit TssM 
26PSPTO_RS13225 (phnC)2823826..2824659 [+], 834499416616phosphonate ABC transporter ATP-binding protein 
27PSPTO_RS13230 (phnD)2824697..2825707 [+], 1011494457181phosphonate ABC transporter substrate-binding protein 
28PSPTO_RS13235 (phnE)2825735..2826523 [+], 789494457180phosphonate ABC transporter, permease protein PhnE 
29PSPTO_RS13240 (phnF)2826562..2827281 [+], 720499416617phosphonate metabolism transcriptional regulator PhnF 
30PSPTO_RS13245 (phnG)2827296..2827760 [+], 465494457176phosphonate C-P lyase system protein PhnG 
31PSPTO_RS13250 (phnH)2827760..2828356 [+], 597499416618phosphonate C-P lyase system protein PhnH 
32PSPTO_RS132552828356..2829435 [+], 1080499416619carbon-phosphorus lyase complex subunit PhnI 
33PSPTO_RS132602829432..2830319 [+], 888499416620alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase PhnJ 
34PSPTO_RS13265 (phnK)2830316..2831137 [+], 822499416621phosphonate C-P lyase system protein PhnK 
35PSPTO_RS13270 (phnL)2831170..2831886 [+], 717499416622phosphonate C-P lyase system protein PhnL 
36PSPTO_RS132752831880..2833025 [+], 1146499416623alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 
37PSPTO_RS13280 (phnN)2833025..2833591 [+], 567499416624phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN 
38PSPTO_RS13285 (phnP)2833582..2834331 [+], 750499416625phosphonate metabolism protein PhnP 
 
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.
 






N/A
N/A
(1) Haapalainen M et al. (2012). Hcp2, a Secreted Protein of the Phytopathogen Pseudomonas syringae pv. Tomato DC3000, Is Required for Fitness for Competition against Bacteria and Yeasts. J Bacteriol. 194(18):4810-22. [PudMed:22753062] experimental
(2) Barret M et al. (2011). Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. Microbiology. 157(Pt 6):1726-39. [PudMed:21474537] in_silico
(3) Sarris PF et al. (2010). In silico analysis reveals multiple putative type VI secretion systems and effector proteins in Pseudomonas syringae pathovars. Mol Plant Pathol. 11(6):795-804. [PudMed:21091602] in_silico
(4) 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