I. Summary
SecReT6 ID14 insolico
StrainPseudomonas putida KT2440
Repliconchromosome [Browse all T6SS(s) in this replicon]
T6SS TypeType i; subtype i4b
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
1PP_30813466346..3466822 [-], 47726989800PEBP family protein 
2PP_30823467336..3468700 [-], 136526989801major facilitator superfamily protein 
3PP_30833469061..3469936 [+], 87626989802auxin efflux carrier 
4PP_30843470069..3472528 [-], 246026989803TonB-dependent siderophore receptor 
5PP_30853472636..3473601 [-], 96626989804transmembrane sensor 
6PP_30863473598..3474104 [-], 50726989805RNA polymerase sigma-70 factor 
7PP_30873474193..3476709 [-], 251726989806excinuclease ABC subunit A 
8PP_30883476877..3477962 [-], 108626989807hypothetical protein  TssA
9PP_30893478058..3478600 [-], 54326989808hypothetical protein  TssD
10PP_30903478720..3481215 [-], 249626989809OmpA domain-containing protein  TssM
11PP_30913482117..3485920 [-], 380426989810hypothetical protein  TssM
12PP_30923485951..3486667 [-], 71726989811hypothetical protein  TssL
13PP_30933486664..3488007 [-], 134426989812hypothetical protein  TssK
14PP_30943488004..3488726 [-], 72326989813hypothetical protein  TssJ
15PP_30953488751..3491387 [-], 263726989814chaperone-associated ATPase  TssH
16PP_30963491345..3492415 [-], 107126989815hypothetical protein  TssG
17PP_30973492379..3494199 [-], 182126989816hypothetical protein  TssF
18PP_30983494199..3494681 [-], 48326989817hypothetical protein  TssE
19PP_30993494708..3496210 [-], 150326989818hypothetical protein  TssC
20PP_31003496225..3496800 [-], 57626989819hypothetical protein  TssB
21PP_31013498998..3499780 [+], 78326989820ADP-ribosylglycohydrolase 
22PP_31023504272..3504568 [-], 29726989821hypothetical 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

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1PP_30893478058..3478600 [-], 54326989808hypothetical protein Psyr_4965

Download FASTA format files
Proteins        Genes
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