SecReT6
I. Summary
SecReT6 ID35 experimental
StrainPseudomonas protegens Pf-5
Repliconchromosome [Browse all T6SS(s) in this replicon]
AccessionNC_004129
Location6897920..6930515
CommentT6-secretion of a peptidoglycan amidase enzyme (antibacterial activity of T6SS implied)
Functionanti-bacterial; effector translocation
T6SS TypeType i; subtype i3
experimental Experimental investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111111111
ComponentTssGTssJTssKTssM
Number1111
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1PFL_RS307806893219..6894619 [+], 1401499376662HDOD domain-containing protein 
2PFL_RS307856894678..6895061 [-], 384505450373hypothetical protein 
3PFL_RS307906895202..6896131 [-], 930499376664hypothetical protein 
4PFL_RS307956896215..6897927 [-], 1713499376665SUMF1/EgtB/PvdO family nonheme iron enzyme 
5PFL_RS308006897920..6899122 [-], 1203499376666ABC transporter permease 
6PFL_RS308056899122..6899838 [-], 717499376667ABC transporter ATP-binding protein 
7PFL_RS308106899838..6902921 [-], 3084499376668protein kinase 
8PFL_RS308156902924..6903658 [-], 735499376669serine/threonine-protein phosphatase 
9PFL_RS30820 (tagF)6903659..6904312 [-], 654499376670type VI secretion system-associated protein TagF 
10PFL_RS30825 (tssM)6904309..6907815 [-], 3507499376671type VI secretion system membrane subunit TssM 
11PFL_RS308306907812..6909137 [-], 1326499376672DotU family type VI secretion system protein 
12PFL_RS30835 (tssK)6909144..6910478 [-], 1335499376673type VI secretion system baseplate subunit TssK 
13PFL_RS30840 (tssJ)6910494..6911000 [-], 507499376674type VI secretion system lipoprotein TssJ 
14PFL_RS30845 (tagH)6911065..6912549 [-], 1485499376675type VI secretion system-associated FHA domain protein TagH 
15PFL_RS30850 (tssA)6912942..6913961 [+], 1020499376676type VI secretion system protein TssA 
16PFL_RS30855 (tssB)6914043..6914558 [+], 516499376677type VI secretion system contractile sheath small subunit 
17PFL_RS30860 (tssC)6914575..6916068 [+], 1494499376678type VI secretion system contractile sheath large subunit 
18PFL_RS308656916187..6916675 [+], 489499376679type VI secretion system tube protein Hcp 
19PFL_RS30870 (tssE)6916836..6917351 [+], 516499376680type VI secretion system baseplate subunit TssE 
20PFL_RS30875 (tssF)6917348..6919207 [+], 1860499376681type VI secretion system baseplate subunit TssF 
21PFL_RS30880 (tssG)6919171..6920223 [+], 1053499376682type VI secretion system baseplate subunit TssG 
22PFL_RS30885 (tssH)6920216..6922891 [+], 2676499376683type VI secretion system ATPase TssH 
23PFL_RS308906923022..6924959 [+], 1938499376684type VI secretion system tip protein VgrG 
24PFL_RS308956924978..6925403 [+], 426499376685DUF1795 domain-containing protein 
25PFL_RS309006925413..6929873 [+], 4461499376686RHS domain-containing protein 
26PFL_RS309056929889..6930515 [+], 627499376687hypothetical protein 
27PFL_RS309106930535..6930798 [-], 264751653559hypothetical protein 
28PFL_RS309156930853..6931287 [-], 435499376689DcrB-related protein 
29PFL_RS309206931399..6931770 [-], 372751653563hypothetical protein 
30PFL_RS309256931758..6932282 [-], 525517922938hypothetical protein 
31PFL_RS309306932447..6932722 [-], 276499376691HU family DNA-binding protein 
32PFL_RS309356932912..6934060 [-], 1149499376692FAD-dependent oxidoreductase 
33PFL_RS309406934103..6934270 [-], 168499376693rubredoxin 
34PFL_RS309456934486..6935049 [+], 564499376694chorismate lyase 
 
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
PA0095 , PFL_3037 (Tge2), PFL_5498 (Tae3), PA0085, PA0091, PFL_6096, PFL_6210

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

Download FASTA format files
Proteins        Genes

Homology Immunity protein list
PFL_3036 (Tgi2), PFL_5499 (Tai3), PFL_6097, PFL_6210

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

Download FASTA format files
Proteins        Genes
Regulatory element identified
GacA
RegulatorDescriptionReference
GacA (PFL_3563)Indirect activatorPMID: 20089046

RetS
RegulatorDescriptionReference
RetS (PFL_0664)RepressorPMID: 23878199

(1) Whitney JC et al. (2013). Identification, structure and function of a novel type VI secretion peptidoglycan glycoside hydrolase effector-immunity pair. J Biol Chem. 288(37):26616-24. [PudMed:23878199] experimental
(2) Loper JE et al. (2012). Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions. PLoS Genet. 8(7):e1002784. [PudMed:22792073] in_silico
(3) Russell AB et al. (2012). A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host Microbe. 11(5):538-49. [PudMed:22607806] experimental in_silico
(4) 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
(5) Hassan KA et al. (2010). Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences. Environ Microbiol. 12(4):899-915. [PudMed:20089046]
 
experimental This literature contains experimental investigation
in_silico This literature contains bioinformatics investigation

Genomics & Bioinformatics Group in MML, SJTU