SecReT6
I. Summary
SecReT6 ID539 insolico
StrainPseudomonas fluorescens F113
Repliconchromosome [Browse all T6SS(s) in this replicon]
AccessionNC_016830
Location2807673..2826705
Comment
FunctionN/A
T6SS TypeType i; subtype i4a
insolico Bioinformatics investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111111111
ComponentTssGTssJTssKTssM
Number1011
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III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1PSF113_24042803210..2804325 [-], 1116378950320Myo-inositol 2-dehydrogenase 
2PSF113_24052804550..2805317 [-], 768378950321short-chain dehydrogenase/reductase family oxidoreductase 
3PSF113_24062805342..2806409 [-], 1068378950322aminoglycoside phosphotransferase 
4PSF113_24072806608..2807003 [+], 396378950323hypothetical protein 
5PSF113_24082807117..2807659 [-], 543378950324phophatidylinositol-4-phosphate 5-kinase 
6PSF113_2409 (vgrG)2807673..2809682 [-], 2010378950325protein VgrG  TssI
7PSF113_24102809694..2810260 [-], 567378950326hypothetical protein 
8PSF113_2411 (clpB)2810386..2812929 [-], 2544378950327chaperone ClpB  TssH
9PSF113_2412 (impH)2812931..2813956 [-], 1026378950328protein ImpH  TssG
10PSF113_2413 (impG)2813920..2815710 [-], 1791378950329protein ImpG  TssF
11PSF113_2414 (impF)2815694..2816137 [-], 444378950330protein ImpF  TssE
12PSF113_2415 (impD)2816151..2816648 [-], 498378950331protein ImpD  TssD
13PSF113_2416 (impC)2816880..2818361 [-], 1482378950332protein ImpC  TssC
14PSF113_2417 (impB)2818392..2818952 [-], 561378950333protein ImpB  TssB
15PSF113_2418 (tssJ3)2819177..2819626 [+], 450378950334protein TssJ3 
16PSF113_2419 (impJ)2819691..2821022 [+], 1332378950335protein ImpJ  TssK
17PSF113_2420 (dotU3)2821041..2821805 [+], 765378950336protein DotU3  TssL
18PSF113_2421 (icmF3)2821802..2825626 [+], 3825378950337protein IcmF3  TssM
19PSF113_2422 (impA)2825623..2826705 [+], 1083378950338protein ImpA  TssA
20PSF113_24232826702..2827655 [-], 954378950339d-isomer specific 2-hydroxyacid dehydrogenase family protein 
21PSF113_24242828467..2829747 [+], 1281378950340threonine serine transporter 
 
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
PSPTO_5435 , PA0095

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1PSF113_1976(hcp2)2318202..2318702 [-], 501378949895protein Hcp2 PSPTO_5435
2PSF113_2885(vgrG1b)3396141..3398366 [+], 2226378950796protein VgrG1b PA0095

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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