SecReT6
I. Summary
SecReT6 ID540 insolico
StrainPseudomonas fluorescens F113
Repliconchromosome [Browse all T6SS(s) in this replicon]
AccessionNC_016830
Location6672386..6694009
Comment
FunctionN/A
T6SS TypeType i; subtype i3
insolico Bioinformatics investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111111111
ComponentTssGTssJTssKTssM
Number1111
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III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1PSF113_5789 (ppkA)6667897..6671007 [-], 3111378953670protein PpkA  PpkA
2PSF113_5790 (pppA)6671004..6671681 [-], 678378953671protein PppA  PppA
3PSF113_5791 (impM)6671736..6672389 [-], 654378953672protein ImpM  TagF
4PSF113_5792 (icmF1)6672386..6675886 [-], 3501378953673protein IcmF1  TssM
5PSF113_5793 (impK)6675883..6677193 [-], 1311378953674protein ImpK  TssL
6PSF113_5794 (impJ2)6677200..6678534 [-], 1335378953675protein ImpJ  TssK
7PSF113_5795 (vasD)6678550..6679056 [-], 507378953676protein VasD  TssJ
8PSF113_5796 (impI)6679125..6680555 [-], 1431378953677protein ImpI  Fha
9PSF113_5797 (impA2)6681052..6682089 [+], 1038378953678protein ImpA  TssA
10PSF113_5798 (impB2)6682171..6682677 [+], 507378953679protein ImpB  TssB
11PSF113_5799 (impC2)6682674..6684176 [+], 1503378953680protein ImpC  TssC
12PSF113_5800 (impD2)6684399..6684887 [+], 489378953681protein ImpD  TssD
13PSF113_58016684969..6685418 [+], 450378953682hypothetical protein 
14PSF113_58026685607..6685855 [+], 249378953683hypothetical protein 
15PSF113_5803 (impF2)6685849..6686361 [+], 513378953684protein ImpF  TssE
16PSF113_5804 (impG2)6686358..6688217 [+], 1860378953685protein ImpG  TssF
17PSF113_5805 (impH2)6688232..6689230 [+], 999378953686protein ImpH  TssG
18PSF113_5806 (clpB3)6689223..6691913 [+], 2691378953687chaperone ClpB  TssH
19PSF113_5807 (vgrG1a)6692072..6694009 [+], 1938378953688protein VgrG1a  TssI
20PSF113_58086694028..6694462 [+], 435378953689hypothetical protein 
21PSF113_58096694475..6698914 [+], 4440378953690Rhs-family protein  PAAR
 
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
PA0085 , PA0091

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1PSF113_5800(impD2)6684399..6684887 [+], 489378953681protein ImpD PA0085
2PSF113_5807(vgrG1a)6692072..6694009 [+], 1938378953688protein VgrG1a PA0091

Download FASTA format files
Proteins        Genes
N/A
(1) Redondo-Nieto M et al. (2013). Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction. BMC Genomics. 14:54. [PudMed:23350846] 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
 
in_silico This literature contains bioinformatics investigation