I. Summary

SecReT6 ID	41
Strain	Pseudomonas syringae pv. tomato str. DC3000
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_004578
Location	2796816..2829435
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	1	1	1	1	0	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	PSPTO_2528	2792008..2792637 [-], 630	28869721	membrane protein
2	PSPTO_2529	2793112..2793453 [-], 342	28869722	FKBP-type peptidyl-prolyl cis-trans isomerase
3	PSPTO_2530	2793450..2793578 [-], 129	28869723	hypothetical protein
4	PSPTO_2531	2793591..2793875 [-], 285	28869724	hypothetical protein
5	PSPTO_2532	2794541..2796109 [+], 1569	28869725	membrane protein, TerC family
6	PSPTO_2533	2796179..2796754 [-], 576	28869726	GNAT family acetyltransferase
7	PSPTO_2534	2796816..2797496 [-], 681	28869727	hypothetical protein
8	PSPTO_2535	2797493..2800933 [-], 3441	28869728	hypothetical protein
9	PSPTO_2536	2800881..2801324 [-], 444	28869729	hypothetical protein
10	PSPTO_2537	2801296..2801763 [-], 468	28869730	hypothetical protein
11	PSPTO_2538	2801756..2803798 [-], 2043	28869731	Rhs element Vgr protein	TssI
12	PSPTO_2539 (hcp-1)	2803874..2804389 [-], 516	28869732	secreted protein Hcp	TssD
13	PSPTO_2541	2806011..2806988 [-], 978	28869733	ISPssy, transposase
14	PSPTO_2543	2807665..2808165 [+], 501	28869734	hypothetical protein	TssB
15	PSPTO_2544	2808195..2809670 [+], 1476	28869735	hypothetical protein	TssC
16	PSPTO_2545	2809686..2810093 [+], 408	28869736	hypothetical protein	TssE
17	PSPTO_2546	2810191..2811978 [+], 1788	28869737	hypothetical protein	TssF
18	PSPTO_2547	2811942..2812949 [+], 1008	28869738	hypothetical protein	TssG
19	PSPTO_2548	2812959..2815562 [+], 2604	28869739	clpB protein	TssH
20	PSPTO_2549	2815564..2817093 [+], 1530	28869740	sigma-54 dependent transcriptional regulator	Sfa2
21	PSPTO_2550	2817143..2817283 [+], 141	28869741	hypothetical protein
22	PSPTO_2551	2817337..2817828 [+], 492	28869742	hypothetical protein	TssJ
23	PSPTO_2552	2817858..2819156 [+], 1299	28869743	hypothetical protein	TssK
24	PSPTO_2553	2819156..2820028 [+], 873	28869744	hypothetical protein	TssL
25	PSPTO_2554	2820042..2823548 [+], 3507	28869745	hypothetical protein	TssM
26	PSPTO_2555 (phnC)	2823826..2824659 [+], 834	28869746	phosphonates ABC transporter ATP-binding protein
27	PSPTO_2556 (phnD)	2824697..2825707 [+], 1011	28869747	phosphonates ABC transporter periplasmic phosphonates-binding protein
28	PSPTO_2557 (phnE)	2825735..2826523 [+], 789	28869748	phosphonates ABC transporter permease
29	PSPTO_2558 (phnF)	2826562..2827281 [+], 720	28869749	transcriptional regulator PhnF
30	PSPTO_2559 (phnG)	2827296..2827760 [+], 465	28869750	phosphonate metabolism protein PhnG
31	PSPTO_2560 (phnH)	2827760..2828356 [+], 597	28869751	PhnH protein
32	PSPTO_2561 (phnI)	2828356..2829435 [+], 1080	28869752	phosphonate metabolism protein PhnI
33	PSPTO_2562 (phnJ)	2829432..2830319 [+], 888	28869753	phosphonate metabolism protein PhnJ
34	PSPTO_2563	2830316..2831137 [+], 822	28869754	phosphonate C-P lyase system protein PhnK
35	PSPTO_2564	2831170..2831886 [+], 717	28869755	phosphonate ABC transporter ATPase
36	PSPTO_2565	2831880..2833025 [+], 1146	28869756	phosphonate metabolism protein PhnM
37	PSPTO_2566 (phnN)	2833025..2833591 [+], 567	28869757	ATP-binding protein PhnN
38	PSPTO_2567	2833582..2834331 [+], 750	28869758	phosphonate metabolism protein, PhnP

 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):

N/A

N/A

(1) Haapalainen M et al. (2012). Hcp2, a Secreted Protein of the Phytopathogen Pseudomonas syringae pv. Tomato DC3000, Is Required for Fitness for Competition against Bacteria and Yeasts. J Bacteriol. 194(18):4810-22. [PudMed:22753062]

(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]

(3) Sarris PF et al. (2010). In silico analysis reveals multiple putative type VI secretion systems and effector proteins in Pseudomonas syringae pathovars. Mol Plant Pathol. 11(6):795-804. [PudMed:21091602]

(4) 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 experimental investigation

This literature contains bioinformatics investigation