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_RS21100	4586132..4587814 [-], 1683	499257316	AMP-binding protein
2	PP_RS21105	4588136..4589299 [+], 1164	489344165	isovaleryl-CoA dehydrogenase
3	PP_RS21110	4589319..4590926 [+], 1608	499257318	propionyl-CoA carboxylase
4	PP_RS21115	4590930..4591745 [+], 816	489344168	gamma-carboxygeranoyl-CoA hydratase
5	PP_RS21120	4591742..4593694 [+], 1953	499257319	acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
6	PP_RS21125	4593993..4594697 [-], 705	499257320	helix-turn-helix domain-containing protein
7	PP_RS21130	4594785..4595084 [+], 300	499257321	hypothetical protein
8	PP_RS21135	4595533..4596048 [+], 516	499257322	DUF4880 domain-containing protein
9	PP_RS21140 (tssM)	4596182..4599808 [-], 3627	499257323	type VI secretion system membrane subunit TssM
10	PP_RS21145 (tssA)	4599805..4601271 [-], 1467	499257324	type VI secretion system protein TssA
11	PP_RS21150 (tagO)	4601259..4601891 [-], 633	499257325	type VI secretion system-associated protein TagO
12	PP_RS21155 (tssB)	4602166..4602669 [+], 504	499257326	type VI secretion system contractile sheath small subunit
13	PP_RS21160 (tssC)	4602687..4604174 [+], 1488	pseudogene	type VI secretion system contractile sheath large subunit
14	PP_RS21165 (tssE)	4604171..4604581 [+], 411	499257327	type VI secretion system baseplate subunit TssE
15	PP_RS21170 (tssF)	4604585..4606351 [+], 1767	499257328	type VI secretion system baseplate subunit TssF
16	PP_RS21175 (tssG)	4606315..4607331 [+], 1017	499257329	type VI secretion system baseplate subunit TssG
17	PP_RS21180 (tssJ)	4607328..4608125 [+], 798	499257330	type VI secretion system lipoprotein TssJ
18	PP_RS21185 (tssK)	4608175..4609512 [+], 1338	489344200	type VI secretion system baseplate subunit TssK
19	PP_RS21190 (icmH)	4609514..4610389 [+], 876	916468577	type IVB secretion system protein IcmH/DotU
20	PP_RS21195	4610523..4611038 [+], 516	499257332	Hcp family type VI secretion system effector
21	PP_RS21200 (tssI)	4611113..4613097 [+], 1985	pseudogene	type VI secretion system tip protein VgrG
22	PP_RS21205	4613145..4613576 [+], 432	499257333	DUF1795 domain-containing protein
23	PP_RS21210	4613630..4618222 [+], 4593	499257334	RHS domain-containing protein
24	PP_RS21215	4618246..4618731 [+], 486	1002826573	SMI1/KNR4 family protein
25	PP_RS28360	4619179..4619610 [+], 432	1818426227	hypothetical protein
26	PP_RS21225	4619633..4619913 [+], 281	pseudogene	transposase
27	PP_RS21230	4620991..4621407 [+], 417	1002826574	putative phosphotriesterase

 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.

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

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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