SecReT6
I. Summary
SecReT6 ID97 insolico
StrainPseudomonas fluorescens Pf0-1
Repliconchromosome [Browse all T6SS(s) in this replicon]
AccessionNC_007492
Location3871434..3902669
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
1Pfl01_33903866698..3867984 [-], 128777459612periplasmic sensor Signal transduction histidine kinase 
2Pfl01_33913867985..3868692 [-], 70877459613two component transcriptional regulator 
3Pfl01_33923868833..3869441 [-], 60977459614tRNA--hydroxylase 
4Pfl01_33933869601..3870464 [+], 86477459615hypothetical protein 
5Pfl01_33943870510..3871019 [-], 51077459616hypothetical protein 
6Pfl01_33953871434..3874058 [+], 2625255961273bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 
7Pfl01_33963874222..3875502 [-], 128177459618aromatic amino acid permease 
8Pfl01_33973875758..3875949 [-], 19277459619hypothetical protein 
9Pfl01_33983876003..3876272 [+], 27077459620hypothetical protein 
10Pfl01_33993876432..3876815 [+], 384774596214-oxalocrotonate tautomerase 
11Pfl01_34003876988..3877956 [+], 969774596222-hydroxyacid dehydrogenase 
12Pfl01_34013877953..3879041 [-], 108977459623ImpA-like protein  TssA
13Pfl01_34023879038..3882859 [-], 382277459624hypothetical protein  TssM
14Pfl01_34033882856..3883620 [-], 76577459625hypothetical protein  TssL
15Pfl01_34043883639..3884970 [-], 133277459626hypothetical protein  TssK
16Pfl01_34053885017..3885463 [-], 44777459627hypothetical protein 
17Pfl01_34063885692..3886234 [+], 54377459628hypothetical protein  TssB
18Pfl01_34073886264..3887748 [+], 148577459629hypothetical protein  TssC
19Pfl01_34083887825..3888322 [+], 49877459630hypothetical protein  TssD
20Pfl01_34093888338..3888781 [+], 44477459631hypothetical protein  TssE
21Pfl01_34103888789..3890558 [+], 177077459632hypothetical protein  TssF
22Pfl01_34113890522..3891547 [+], 102677459633hypothetical protein  TssG
23Pfl01_34123891549..3894089 [+], 254177459634ClpA/B-type protease  TssH
24Pfl01_34133894106..3894720 [+], 61577459635hypothetical protein 
25Pfl01_34143894859..3895743 [+], 88577459636hypothetical protein 
26Pfl01_34153895804..3897813 [+], 201077459637Rhs element Vgr protein  TssI
27Pfl01_34163897826..3898368 [+], 54377459638hypothetical protein 
28Pfl01_34173898370..3898792 [-], 42377459639hypothetical protein 
29Pfl01_34183898956..3900023 [+], 106877459640aminoglycoside phosphotransferase 
30Pfl01_34193900062..3900829 [+], 76877459641short chain dehydrogenase 
31Pfl01_34203900875..3901477 [-], 60377459642hypothetical protein 
32Pfl01_34213902068..3902430 [-], 36377459643hypothetical protein 
33Pfl01_34223902427..3902669 [-], 24377459644hypothetical protein 
34Pfl01_34233902860..3904350 [-], 149177459645sensor protein 
35Pfl01_34243904428..3905318 [-], 89177459646LysR family transcriptional regulator 
36Pfl01_34253905325..3907532 [-], 220877459647twin-arginine translocation pathway signal protein 
 
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
PSPTO_5435 , PSPTO_5435

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1Pfl01_20452330996..2331511 [-], 51677458272hypothetical protein PSPTO_5435
2Pfl01_23282683657..2684172 [+], 51677458555hypothetical protein PSPTO_5435

Download FASTA format files
Proteins        Genes
N/A
(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