I. Summary

SecReT6 ID	97
Strain	Pseudomonas fluorescens Pf0-1
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_007492
Location	3871434..3902669
Comment
Function	N/A
T6SS Type	Type i; subtype i4a
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	0	1	1

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	Pfl01_3390	3866698..3867984 [-], 1287	77459612	periplasmic sensor Signal transduction histidine kinase
2	Pfl01_3391	3867985..3868692 [-], 708	77459613	two component transcriptional regulator
3	Pfl01_3392	3868833..3869441 [-], 609	77459614	tRNA--hydroxylase
4	Pfl01_3393	3869601..3870464 [+], 864	77459615	hypothetical protein
5	Pfl01_3394	3870510..3871019 [-], 510	77459616	hypothetical protein
6	Pfl01_3395	3871434..3874058 [+], 2625	255961273	bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
7	Pfl01_3396	3874222..3875502 [-], 1281	77459618	aromatic amino acid permease
8	Pfl01_3397	3875758..3875949 [-], 192	77459619	hypothetical protein
9	Pfl01_3398	3876003..3876272 [+], 270	77459620	hypothetical protein
10	Pfl01_3399	3876432..3876815 [+], 384	77459621	4-oxalocrotonate tautomerase
11	Pfl01_3400	3876988..3877956 [+], 969	77459622	2-hydroxyacid dehydrogenase
12	Pfl01_3401	3877953..3879041 [-], 1089	77459623	ImpA-like protein	TssA
13	Pfl01_3402	3879038..3882859 [-], 3822	77459624	hypothetical protein	TssM
14	Pfl01_3403	3882856..3883620 [-], 765	77459625	hypothetical protein	TssL
15	Pfl01_3404	3883639..3884970 [-], 1332	77459626	hypothetical protein	TssK
16	Pfl01_3405	3885017..3885463 [-], 447	77459627	hypothetical protein
17	Pfl01_3406	3885692..3886234 [+], 543	77459628	hypothetical protein	TssB
18	Pfl01_3407	3886264..3887748 [+], 1485	77459629	hypothetical protein	TssC
19	Pfl01_3408	3887825..3888322 [+], 498	77459630	hypothetical protein	TssD
20	Pfl01_3409	3888338..3888781 [+], 444	77459631	hypothetical protein	TssE
21	Pfl01_3410	3888789..3890558 [+], 1770	77459632	hypothetical protein	TssF
22	Pfl01_3411	3890522..3891547 [+], 1026	77459633	hypothetical protein	TssG
23	Pfl01_3412	3891549..3894089 [+], 2541	77459634	ClpA/B-type protease	TssH
24	Pfl01_3413	3894106..3894720 [+], 615	77459635	hypothetical protein
25	Pfl01_3414	3894859..3895743 [+], 885	77459636	hypothetical protein
26	Pfl01_3415	3895804..3897813 [+], 2010	77459637	Rhs element Vgr protein	TssI
27	Pfl01_3416	3897826..3898368 [+], 543	77459638	hypothetical protein
28	Pfl01_3417	3898370..3898792 [-], 423	77459639	hypothetical protein
29	Pfl01_3418	3898956..3900023 [+], 1068	77459640	aminoglycoside phosphotransferase
30	Pfl01_3419	3900062..3900829 [+], 768	77459641	short chain dehydrogenase
31	Pfl01_3420	3900875..3901477 [-], 603	77459642	hypothetical protein
32	Pfl01_3421	3902068..3902430 [-], 363	77459643	hypothetical protein
33	Pfl01_3422	3902427..3902669 [-], 243	77459644	hypothetical protein
34	Pfl01_3423	3902860..3904350 [-], 1491	77459645	sensor protein
35	Pfl01_3424	3904428..3905318 [-], 891	77459646	LysR family transcriptional regulator
36	Pfl01_3425	3905325..3907532 [-], 2208	77459647	twin-arginine translocation pathway signal 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

PSPTO_5435 , PSPTO_5435

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	Pfl01_2045	2330996..2331511 [-], 516	77458272	hypothetical protein	PSPTO_5435
2	Pfl01_2328	2683657..2684172 [+], 516	77458555	hypothetical protein	PSPTO_5435

Download FASTA format files

Proteins        Genes

N/A

(1) Loper JE et al. (2012). Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions. PLoS Genet. 8(7):e1002784. [PudMed:22792073]

(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) 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