SecReT6
I. Summary
SecReT6 ID14 insolico
StrainPseudomonas putida KT2440
Repliconchromosome [Browse all T6SS(s) in this replicon]
AccessionNC_002947
Location3470069..3499780
Comment
FunctionN/A
T6SS TypeType i; subtype i4b
insolico Bioinformatics investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111111111
ComponentTssGTssJTssKTssM
Number1112
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1PP_RS159503466349..3466900 [-], 552898330895YbhB/YbcL family Raf kinase inhibitor-like protein 
2PP_RS159553466949..3467257 [-], 309518268253hypothetical protein 
3PP_RS159603467339..3468637 [-], 1299519035062MFS transporter 
4PP_RS159653469064..3469939 [+], 876499256441AEC family transporter 
5PP_RS159703470072..3472489 [-], 2418898330891TonB-dependent receptor 
6PP_RS159753472639..3473601 [-], 963898330889FecR domain-containing protein 
7PP_RS159803473601..3474107 [-], 507499256444sigma-70 family RNA polymerase sigma factor 
8PP_RS159853474196..3476712 [-], 2517499256445excinuclease ABC subunit UvrA 
9PP_RS15990 (tssA)3476880..3477965 [-], 1086499256446type VI secretion system protein TssA 
10PP_RS159953478061..3478579 [-], 519898330886type VI secretion system tube protein Hcp 
11PP_RS16000 (tssM)3478723..3481218 [-], 2496499256448type VI secretion system membrane subunit TssM 
12PP_RS16005 (tagF)3481215..3482123 [-], 909898330884type VI secretion system-associated protein TagF 
13PP_RS160103482120..3485923 [-], 3804499256449hypothetical protein 
14PP_RS16015 (icmH)3485954..3486670 [-], 717499256450type IVB secretion system protein IcmH/DotU 
15PP_RS16020 (tssK)3486667..3488010 [-], 1344499256451type VI secretion system baseplate subunit TssK 
16PP_RS16025 (tssJ)3488007..3488729 [-], 723490713868type VI secretion system lipoprotein TssJ 
17PP_RS16030 (tssH)3488754..3491351 [-], 2598898330880type VI secretion system ATPase TssH 
18PP_RS16035 (tssG)3491348..3492418 [-], 1071489341176type VI secretion system baseplate subunit TssG 
19PP_RS16040 (tssF)3492382..3494202 [-], 1821499256453type VI secretion system baseplate subunit TssF 
20PP_RS16045 (tssE)3494202..3494684 [-], 483489341181type VI secretion system baseplate subunit TssE 
21PP_RS16050 (tssC)3494711..3496213 [-], 1503489341182type VI secretion system contractile sheath large subunit 
22PP_RS16055 (tssB)3496228..3496767 [-], 540898331645type VI secretion system contractile sheath small subunit 
23PP_RS160603496832..3497581 [-], 750898330878hypothetical protein 
24PP_RS160653498302..3498853 [-], 552489341191hypothetical protein 
25PP_RS160703499064..3499783 [+], 720pseudogeneADP-ribosylglycohydrolase family protein 
26PP_RS160753500053..3500325 [-], 2731002826534hypothetical protein 
27PP_RS284353500335..3500803 [-], 469pseudogenehypothetical protein 
28PP_RS160853501267..3501455 [+], 189pseudogenetype VI secretion system tip protein VgrG 
29PP_RS160903501614..3502312 [+], 699489341205hypothetical protein 
30PP_RS160953502346..3502605 [+], 260pseudogenehypothetical protein 
31PP_RS283953502579..3502684 [-], 106pseudogenehypothetical protein 
32PP_RS161053502704..3503015 [-], 312898330871hypothetical protein 
33PP_RS161103503425..3503814 [-], 3901160888979reverse transcriptase 
34PP_RS161153503869..3504185 [-], 317pseudogenehypothetical protein 
35PP_RS161203504275..3504571 [-], 297499256456hypothetical 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

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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
Psyr_4965

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog

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Proteins        Genes
N/A
The information on regulator interaction.

#homolog effector locus tagRegulator wayFunctionRegulate targetDescription
1PP_4373 (FleQ)c-di-GMP-K1-T6SS (hcp1) expressionFleQ negatively regulate hcp1 expression at all the growth phases.
2PP_0952 (RopN)c-di-GMP-PP_4373 (FleQ)RopN negatively regulates hcp1 expression at all the growth phases,and interacts a domain characteristic of FleQ.
3PP_0914 (BifA)c-di-GMP+the levels of c-di-GMPBifA, a cyclic-Di-GMP phosphodiesterase can lower the intracellular level of c-di-GMP.
(1) 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
(2) 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