I. Summary
SecReT6 ID502 insolico
StrainPantoea sp. At-9b
Repliconchromosome [Browse all T6SS(s) in this replicon]
T6SS TypeType i; subtype i2
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
1Pat9b_34463780605..3780943 [-], 339317049645putative prophage protein 
2Pat9b_34483781102..3781611 [-], 510317049646regulatory CII family protein 
3Pat9b_34493781646..3781882 [-], 237317049647putative regulator from bacteriophage origin 
4Pat9b_34503781972..3782577 [+], 606317049648CI repressor 
5Pat9b_34513782586..3783617 [+], 1032317049649integrase family protein 
6Pat9b_34523783725..3784483 [+], 759317049650hypothetical protein 
7Pat9b_34533785432..3786475 [-], 1044317049651ImpA domain-containing protein  TssA
8Pat9b_34543786513..3786953 [-], 441317049652type VI secretion system lysozyme-like protein  TssE
9Pat9b_34553786950..3787486 [-], 537317049653type VI secretion lipoprotein  TssJ
10Pat9b_34563787464..3788534 [-], 1071317049654type VI secretion protein  TssG
11Pat9b_34573788498..3790252 [-], 1755317049655type VI secretion protein  TssF
12Pat9b_34583790283..3791860 [-], 1578317049656type VI secretion-associated protein  TssA
13Pat9b_34593791881..3795237 [-], 3357317049657ImcF domain-containing protein  TssM
14Pat9b_34603795292..3797937 [-], 2646317049658type VI secretion ATPase, ClpV1 family  TssH
15Pat9b_34613798067..3798567 [-], 501317049659type VI secretion system effector  TssD
16Pat9b_34623798573..3800159 [-], 1587317049660OmpA/MotB domain-containing protein  TagL
17Pat9b_34633800156..3800836 [-], 681317049661DotU family type IV/VI secretion system protein  TssL
18Pat9b_34643800833..3802173 [-], 1341317049662type VI secretion protein  TssK
19Pat9b_34653802189..3803730 [-], 1542317049663type VI secretion protein  TssC
20Pat9b_34663803769..3804266 [-], 498317049664type VI secretion protein  TssB
21Pat9b_34673804576..3804677 [+], 102317049665hypothetical protein 
22Pat9b_34683804799..3806232 [+], 1434317049666zinc finger C2H2-type domain-containing protein 
23Pat9b_34693806356..3807450 [+], 1095317049667D-alanine--D-alanine ligase 
24Pat9b_34703807455..3808879 [-], 1425317049668diguanylate cyclase 
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
EC042_4529 , SMA3455, SMA3456

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
1Pat9b_34613798067..3798567 [-], 501317049659type VI secretion system effector EC042_4529
2Pat9b_37554094887..4095369 [+], 483317049953type VI secretion system effector SMA3455
3Pat9b_37564095415..4095897 [+], 483317049954type VI secretion system effector SMA3456

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Proteins        Genes
(1) De Maayer P et al. (2011). Comparative genomics of the Type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins. BMC Genomics. 12:576. [PudMed:22115407] in_silico
in_silico This literature contains bioinformatics investigation