I. Summary

SecReT6 ID	55
Strain	Pseudomonas syringae pv. phaseolicola 1448A
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_005773
Location	133108..164447
Comment
Function	N/A
T6SS Type	Type i; subtype i4b
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	0	1	1	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	2

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	PSPPH_0111	128275..128730 [+], 456	71734560	acetyltransferase
2	PSPPH_0112	128727..129446 [+], 720	71735114	hypothetical protein
3	PSPPH_0113	130159..131262 [-], 1104	71736461	ISPsy19, transposase
4	PSPPH_0114	131400..132371 [+], 972	71736075	ISPsy2, transposase
5	PSPPH_0115	132507..133010 [-], 504	71735102	lipoprotein
6	PSPPH_0116	133108..134130 [-], 1023	71734711	lipoprotein
7	PSPPH_0117	134132..136063 [-], 1932	71733687	phospholipase D
8	PSPPH_0118	136114..136368 [-], 255	71733302	hypothetical protein	PAAR
9	PSPPH_0119	136714..137973 [-], 1260	71737316	ISPsy18, transposase
10	PSPPH_0121	138816..139919 [-], 1104	71733734	ImpA-like N-terminal family protein	TssA
11	PSPPH_0122	140006..140524 [-], 519	71737480	hypothetical protein	TssD
12	PSPPH_0123	140680..143172 [-], 2493	71738017	OmpA domain-containing protein	TssM
13	PSPPH_0124	143169..144092 [-], 924	71736066	hypothetical protein
14	PSPPH_0125	144124..148044 [-], 3921	71736620	ImcF-like family protein	TssM
15	PSPPH_0126	148075..148788 [-], 714	71733907	hypothetical protein	TssL
16	PSPPH_0127	148785..150128 [-], 1344	71734452	hypothetical protein	TssK
17	PSPPH_0128	150125..150880 [-], 756	71733359	lipoprotein	TssJ
18	PSPPH_0129 (clpB1)	150906..153509 [-], 2604	71736516	ATP-dependent Clp protease ATP-binding subunit	TssH
19	PSPPH_0130	153506..154576 [-], 1071	71737889	ImpH	TssG
20	PSPPH_0131	154540..156372 [-], 1833	71735418	ImpG	TssF
21	PSPPH_0132	156372..156854 [-], 483	71736251	hypothetical protein	TssE
22	PSPPH_0133	156880..158382 [-], 1503	71734334	hypothetical protein	TssC
23	PSPPH_0134	158397..158930 [-], 534	71734592	hypothetical protein	TssB
24	PSPPH_0135	158999..159883 [-], 885	71737051	hypothetical protein
25	PSPPH_0136	160913..161734 [-], 822	71737586	hypothetical protein
26	PSPPH_0138	163896..164447 [-], 552	71733264	hypothetical protein
27	PSPPH_0139	164567..166903 [-], 2337	71733934	oxidoreductase alpha (molybdopterin) subunit
28	PSPPH_0140 (fdhD)	166900..167736 [-], 837	71734476	formate dehydrogenase accessory protein FdhD
29	PSPPH_0141	167840..168721 [-], 882	71735314	LysR family transcriptional regulator
30	PSPPH_0142	168763..169440 [-], 678	71733682	HAD superfamily hydrolase

 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

Psyr_4965

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	PSPPH_0122	140006..140524 [-], 519	71737480	hypothetical protein	Psyr_4965

Download FASTA format files

Proteins        Genes

N/A

(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