I. Summary

SecReT6 ID	540
Strain	Pseudomonas fluorescens F113
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_016830
Location	6672386..6694009
Comment
Function	N/A
T6SS Type	Type i; subtype i3
Bioinformatics investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	1	1	1	1	1	1	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	1

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	PSF113_5789 (ppkA)	6667897..6671007 [-], 3111	378953670	protein PpkA	PpkA
2	PSF113_5790 (pppA)	6671004..6671681 [-], 678	378953671	protein PppA	PppA
3	PSF113_5791 (impM)	6671736..6672389 [-], 654	378953672	protein ImpM	TagF
4	PSF113_5792 (icmF1)	6672386..6675886 [-], 3501	378953673	protein IcmF1	TssM
5	PSF113_5793 (impK)	6675883..6677193 [-], 1311	378953674	protein ImpK	TssL
6	PSF113_5794 (impJ2)	6677200..6678534 [-], 1335	378953675	protein ImpJ	TssK
7	PSF113_5795 (vasD)	6678550..6679056 [-], 507	378953676	protein VasD	TssJ
8	PSF113_5796 (impI)	6679125..6680555 [-], 1431	378953677	protein ImpI	Fha
9	PSF113_5797 (impA2)	6681052..6682089 [+], 1038	378953678	protein ImpA	TssA
10	PSF113_5798 (impB2)	6682171..6682677 [+], 507	378953679	protein ImpB	TssB
11	PSF113_5799 (impC2)	6682674..6684176 [+], 1503	378953680	protein ImpC	TssC
12	PSF113_5800 (impD2)	6684399..6684887 [+], 489	378953681	protein ImpD	TssD
13	PSF113_5801	6684969..6685418 [+], 450	378953682	hypothetical protein
14	PSF113_5802	6685607..6685855 [+], 249	378953683	hypothetical protein
15	PSF113_5803 (impF2)	6685849..6686361 [+], 513	378953684	protein ImpF	TssE
16	PSF113_5804 (impG2)	6686358..6688217 [+], 1860	378953685	protein ImpG	TssF
17	PSF113_5805 (impH2)	6688232..6689230 [+], 999	378953686	protein ImpH	TssG
18	PSF113_5806 (clpB3)	6689223..6691913 [+], 2691	378953687	chaperone ClpB	TssH
19	PSF113_5807 (vgrG1a)	6692072..6694009 [+], 1938	378953688	protein VgrG1a	TssI
20	PSF113_5808	6694028..6694462 [+], 435	378953689	hypothetical protein
21	PSF113_5809	6694475..6698914 [+], 4440	378953690	Rhs-family protein	PAAR

 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.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

Homology Effector list

PA0085 , PA0091

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	PSF113_5800(impD2)	6684399..6684887 [+], 489	378953681	protein ImpD	PA0085
2	PSF113_5807(vgrG1a)	6692072..6694009 [+], 1938	378953688	protein VgrG1a	PA0091

Download FASTA format files

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]

(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]

This literature contains bioinformatics investigation