I. Summary
SecReT6 ID98 insolico
StrainPseudomonas fluorescens Pf0-1
Repliconchromosome [Browse all T6SS(s) in this replicon]
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
1Pfl01_55646232319..6233311 [-], 99377461785hypothetical protein 
2Pfl01_55656233363..6234118 [-], 75677461786hypothetical protein 
3Pfl01_55666234121..6234939 [-], 81977461787hypothetical protein 
4Pfl01_55676234956..6235384 [-], 42977461788hypothetical protein 
5Pfl01_55686235506..6235961 [-], 45677461789hypothetical protein 
6Pfl01_55696236049..6236534 [-], 48677461790hypothetical protein 
7Pfl01_55706236555..6239005 [-], 245177461791hypothetical protein 
8Pfl01_55716239015..6240409 [-], 139577461792hypothetical protein 
9Pfl01_55726240486..6241364 [-], 87977461793hypothetical protein 
10Pfl01_55736241361..6242368 [-], 100877461794hypothetical protein 
11Pfl01_55746242365..6244590 [-], 222677461795Rhs element Vgr protein  TssI
12Pfl01_55756244619..6245620 [-], 100277461796Serine/threonine protein kinase  Stk1
13Pfl01_55766245617..6246345 [-], 72977461797Ser/Thr phosphatase  Stp1
14Pfl01_55776246345..6249884 [-], 354077461798hypothetical protein  TssM
15Pfl01_55786249898..6250773 [-], 87677461799hypothetical protein  TssL
16Pfl01_55796250779..6252110 [-], 133277461800hypothetical protein  TssK
17Pfl01_55806252113..6252613 [-], 50177461801lipoprotein  TssJ
18Pfl01_55816252619..6253812 [-], 119477461802FHA domain-containing protein  Fha
19Pfl01_55826253831..6253995 [-], 16577461803hypothetical protein 
20Pfl01_55836254065..6255591 [-], 152777461804Fis family transcriptional regulator  Sfa2
21Pfl01_55846255602..6258259 [-], 265877461805ClpB protein  TssH
22Pfl01_55856258271..6259197 [-], 92777461806hypothetical protein  TssG
23Pfl01_55866259242..6261029 [-], 178877461807hypothetical protein  TssF
24Pfl01_55876261057..6261488 [-], 43277461808hypothetical protein 
25Pfl01_55886261506..6261949 [-], 44477461809hypothetical protein 
26Pfl01_55896261946..6262350 [-], 40577461810hypothetical protein 
27Pfl01_55906262347..6262730 [-], 38477461811hypothetical protein 
28Pfl01_55916262751..6263134 [-], 38477461812hypothetical protein 
29Pfl01_55926263127..6264536 [-], 141077461813hypothetical protein  PAAR
30Pfl01_55936264548..6264955 [-], 40877461814hypothetical protein  TssE
31Pfl01_55946264965..6266440 [-], 147677461815hypothetical protein  TssC
32Pfl01_55956266469..6266972 [-], 50477461816hypothetical protein  TssB
33Pfl01_55966267005..6268567 [-], 156377461817ImpA-like protein  TssA
34Pfl01_55976269283..6272639 [+], 335777461818Rhs element Vgr protein  TssI
35Pfl01_55986272632..6273303 [+], 67277461819hypothetical protein 
36Pfl01_55996273334..6273786 [+], 45377461820hypothetical protein 
37Pfl01_56006273921..6274196 [-], 27677461821nucleoid protein HU subunit alpha 
38Pfl01_56016274387..6275535 [-], 114977461822FAD-dependent pyridine nucleotide-disulfide oxidoreductase 
39Pfl01_56026275557..6275724 [-], 16877461823rubredoxin-type Fe(Cys)4 protein 
40Pfl01_56036275924..6276475 [+], 55277461824chorismate lyase 
41Pfl01_5604 (ubiA)6276475..6277365 [+], 891774618254-hydroxybenzoate octaprenyltransferase 
42Pfl01_56056277417..6277800 [-], 38477461826hypothetical protein 
43Pfl01_56066277952..6278641 [+], 69077461827two component transcriptional regulator 
44Pfl01_56076278680..6280002 [+], 132377461828PAS/PAC sensor Signal transduction histidine kinase 
45Pfl01_56086280114..6281454 [+], 134177461829hypothetical protein 
46Pfl01_56096281461..6282357 [-], 89777461830peptidase M23B 
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.

(1) 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
(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) 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
in_silico This literature contains bioinformatics investigation