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
13
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1PFL_60726893219..6894619 [+], 140170733355HDOD domain-containing protein 
2PFL_60736894678..6895166 [-], 48970733356hypothetical protein 
3PFL_6074 (tagQ)6895202..6896131 [-], 930346643325type VI secretion-associated lipoprotein TagQ  TagQ
4PFL_6075 (tagR)6896215..6897927 [-], 171370733358type VI secretion posttranslational regulatory protein TagR  TagR
5PFL_6076 (tagS)6897920..6899122 [-], 120370733359Lol-like lipoprotein-translocating system, transmembrane protein TagS  TagS
6PFL_6077 (tagT)6899122..6899838 [-], 71770733360Lol-like lipoprotein-translocating system, ATP-binding protein TagT  TagT
7PFL_6078 (ppkA)6899838..6902921 [-], 3084346643326serine/threonine protein kinase PpkA  PpkA
8PFL_6079 (pppA)6902924..6903658 [-], 73570733362serine/threonine phosphoprotein phosphatase PppA  PppA
9PFL_6080 (tagF)6903659..6904312 [-], 65470733363type VI secretion-associated protein TagF  TagF
10PFL_6081 (tssM)6904309..6907815 [-], 350770733364type VI secretion protein TssM  TssM
11PFL_6082 (tssL)6907812..6909137 [-], 132670733365hypothetical protein  TssL
12PFL_6083 (tssK)6909144..6910478 [-], 133570733366type VI secretion protein TssK  TssK
13PFL_6084 (tssJ)6910494..6911000 [-], 50770733367type VI secretion lipoprotein TssJ  TssJ
14PFL_6085 (fha)6911065..6912549 [-], 148570733368type VI secretion protein Fha  Fha
15PFL_6086 (tssA)6912942..6913961 [+], 1020346643327type VI secretion protein TssA  TssA
16PFL_6087 (tssB)6914043..6914558 [+], 51670733370type VI secretion protein TssB  TssB
17PFL_6088 (tssC)6914575..6916068 [+], 149470733371type VI secretion protein TssC  TssC
18PFL_6089 (hcp)6916187..6916675 [+], 48970733372type VI secretion system effector Hcp  TssD
19PFL_6090 (tssE)6916836..6917351 [+], 516346643328type VI secretion protein TssE  TssE
20PFL_6091 (tssF)6917348..6919207 [+], 186070733374type VI secretion protein TssF  TssF
21PFL_6092 (tssG)6919171..6920223 [+], 105370733375type VI secretion protein TssG  TssG
22PFL_6093 (clpV)6920216..6922891 [+], 267670733376type VI secretion ATPase ClpV  TssH
23PFL_6094 (vgrG)6923022..6924959 [+], 193870733377type VI secretion protein VgrG  TssI
24PFL_60956924978..6925403 [+], 42670733378hypothetical protein 
25PFL_60966925413..6929873 [+], 446170733379Rhs family protein  PAAR
26PFL_60976929889..6930515 [+], 62770733380hypothetical protein 
27PFL_60986930535..6930828 [-], 29470733381hypothetical protein 
28PFL_60996930853..6931287 [-], 43570733382hypothetical protein 
29PFL_61006931399..6932253 [-], 855346643329lipoprotein 
30PFL_6102 (hupA)6932447..6932722 [-], 27670733385DNA-binding protein HU subunit alpha 
31PFL_6103 (rubB)6932912..6934060 [-], 114970733386rubredoxin-NAD(+) reductase 
32PFL_6104 (rubA)6934103..6934270 [-], 16870733387rubredoxin 
33PFL_6105 (ubiC)6934486..6935049 [+], 56470733388chorismate 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

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
PA0095 , PFL_3037 (Tge2), PFL_5498 (Tae3), PA0085, PA0091, PFL_6096, PFL_6210

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1PFL_30043452885..3455134 [-], 225070730371ImpA family type VI secretion-associated protein PA0095
2PFL_30373502760..3503293 [-], 53470730402hypothetical protein (Tge2)PFL_3037 (Tge2)
3PFL_54986278373..6278744 [+], 37270732799hypothetical protein (Tae3)PFL_5498 (Tae3)
4PFL_6089(hcp)6916187..6916675 [+], 48970733372type VI secretion system effector Hcp PA0085
5PFL_6094(vgrG)6923022..6924959 [+], 193870733377type VI secretion protein VgrG PA0091
6PFL_60966925413..6929873 [+], 446170733379Rhs family protein PFL_6096
7PFL_62107050414..7050875 [+], 46270733493hypothetical protein PFL_6210
Data from experimental literature

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
1PFL_30363502296..3502766 [-], 47170730401lipoprotein (Tgi2)PFL_3036 (Tgi2)
2PFL_54996278755..6279204 [+], 45070732800hypothetical protein (Tai3)PFL_5499 (Tai3)
3PFL_60976929889..6930515 [+], 62770733380hypothetical protein PFL_6097
4PFL_62107050414..7050875 [+], 46270733493hypothetical protein PFL_6210
Data from experimental literature

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