I. Summary

SecReT6 ID	15
Strain	Pseudomonas putida KT2440
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_002947
Location	4590927..4618219
Comment
Function	N/A
T6SS Type	Type i; subtype i1
Bioinformatics investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	0	1	1	0	0	1	0	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	PP_4063	4586129..4587811 [-], 1683	26990764	AMP-binding protein
2	PP_4064 (ivd)	4588022..4589296 [+], 1275	26990765	acyl-CoA dehydrogenase
3	PP_4065	4589316..4590923 [+], 1608	26990766	propionyl-CoA carboxylase
4	PP_4066	4590927..4591742 [+], 816	26990767	gamma-carboxygeranoyl-CoA hydratase
5	PP_4067	4591739..4593691 [+], 1953	26990768	acetyl-CoA carboxylase, biotin carboxylase
6	PP_4068	4593990..4594694 [-], 705	26990769	Cro/CI family transcriptional regulator
7	PP_4069	4594782..4595081 [+], 300	26990770	hypothetical protein
8	PP_4070	4595530..4596045 [+], 516	26990771	hypothetical protein
9	PP_4071	4596179..4599805 [-], 3627	26990772	hypothetical protein	TssM
10	PP_4072	4599802..4601268 [-], 1467	26990773	hypothetical protein
11	PP_4073	4601256..4601888 [-], 633	26990774	hypothetical protein
12	PP_4074	4602163..4602666 [+], 504	26990775	hypothetical protein	TssB
13	PP_4076	4604168..4604578 [+], 411	26990776	hypothetical protein	TssE
14	PP_4077	4604582..4606348 [+], 1767	26990777	hypothetical protein	TssF
15	PP_4078	4606312..4607328 [+], 1017	26990778	hypothetical protein	TssG
16	PP_4079	4607325..4608122 [+], 798	26990779	hypothetical protein	TssJ
17	PP_4080	4608172..4609509 [+], 1338	26990780	hypothetical protein	TssK
18	PP_4081	4609454..4610386 [+], 933	26990781	hypothetical protein	TssL
19	PP_4082 (hcp-2)	4610520..4611035 [+], 516	26990782	hcp protein	TssD
20	PP_4084	4613142..4613573 [+], 432	26990783	hypothetical protein
21	PP_4085	4613627..4618219 [+], 4593	26990784	RHS family protein	PAAR
22	PP_4086	4619477..4620040 [-], 564	26990785	hypothetical protein
23	PP_4087	4620241..4620393 [+], 153	26990786	hypothetical protein

 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

ECA4275

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	PP_4082(hcp-2)	4610520..4611035 [+], 516	26990782	hcp protein	ECA4275

Download FASTA format files

Proteins        Genes

N/A

Regulatory element identified

TurA

Regulator	Description	Reference
TurA (PP_1366)	Indirect repressor	PMID: 19788653

(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]

(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]

This literature contains bioinformatics investigation