I. Summary

SecReT6 ID	98
Strain	Pseudomonas fluorescens Pf0-1
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_007492
Location	6236555..6277800
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	0	1	2	1	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	Pfl01_5564	6232319..6233311 [-], 993	77461785	hypothetical protein
2	Pfl01_5565	6233363..6234118 [-], 756	77461786	hypothetical protein
3	Pfl01_5566	6234121..6234939 [-], 819	77461787	hypothetical protein
4	Pfl01_5567	6234956..6235384 [-], 429	77461788	hypothetical protein
5	Pfl01_5568	6235506..6235961 [-], 456	77461789	hypothetical protein
6	Pfl01_5569	6236049..6236534 [-], 486	77461790	hypothetical protein
7	Pfl01_5570	6236555..6239005 [-], 2451	77461791	hypothetical protein
8	Pfl01_5571	6239015..6240409 [-], 1395	77461792	hypothetical protein
9	Pfl01_5572	6240486..6241364 [-], 879	77461793	hypothetical protein
10	Pfl01_5573	6241361..6242368 [-], 1008	77461794	hypothetical protein
11	Pfl01_5574	6242365..6244590 [-], 2226	77461795	Rhs element Vgr protein	TssI
12	Pfl01_5575	6244619..6245620 [-], 1002	77461796	Serine/threonine protein kinase	Stk1
13	Pfl01_5576	6245617..6246345 [-], 729	77461797	Ser/Thr phosphatase	Stp1
14	Pfl01_5577	6246345..6249884 [-], 3540	77461798	hypothetical protein	TssM
15	Pfl01_5578	6249898..6250773 [-], 876	77461799	hypothetical protein	TssL
16	Pfl01_5579	6250779..6252110 [-], 1332	77461800	hypothetical protein	TssK
17	Pfl01_5580	6252113..6252613 [-], 501	77461801	lipoprotein	TssJ
18	Pfl01_5581	6252619..6253812 [-], 1194	77461802	FHA domain-containing protein	Fha
19	Pfl01_5582	6253831..6253995 [-], 165	77461803	hypothetical protein
20	Pfl01_5583	6254065..6255591 [-], 1527	77461804	Fis family transcriptional regulator	Sfa2
21	Pfl01_5584	6255602..6258259 [-], 2658	77461805	ClpB protein	TssH
22	Pfl01_5585	6258271..6259197 [-], 927	77461806	hypothetical protein	TssG
23	Pfl01_5586	6259242..6261029 [-], 1788	77461807	hypothetical protein	TssF
24	Pfl01_5587	6261057..6261488 [-], 432	77461808	hypothetical protein
25	Pfl01_5588	6261506..6261949 [-], 444	77461809	hypothetical protein
26	Pfl01_5589	6261946..6262350 [-], 405	77461810	hypothetical protein
27	Pfl01_5590	6262347..6262730 [-], 384	77461811	hypothetical protein
28	Pfl01_5591	6262751..6263134 [-], 384	77461812	hypothetical protein
29	Pfl01_5592	6263127..6264536 [-], 1410	77461813	hypothetical protein	PAAR
30	Pfl01_5593	6264548..6264955 [-], 408	77461814	hypothetical protein	TssE
31	Pfl01_5594	6264965..6266440 [-], 1476	77461815	hypothetical protein	TssC
32	Pfl01_5595	6266469..6266972 [-], 504	77461816	hypothetical protein	TssB
33	Pfl01_5596	6267005..6268567 [-], 1563	77461817	ImpA-like protein	TssA
34	Pfl01_5597	6269283..6272639 [+], 3357	77461818	Rhs element Vgr protein	TssI
35	Pfl01_5598	6272632..6273303 [+], 672	77461819	hypothetical protein
36	Pfl01_5599	6273334..6273786 [+], 453	77461820	hypothetical protein
37	Pfl01_5600	6273921..6274196 [-], 276	77461821	nucleoid protein HU subunit alpha
38	Pfl01_5601	6274387..6275535 [-], 1149	77461822	FAD-dependent pyridine nucleotide-disulfide oxidoreductase
39	Pfl01_5602	6275557..6275724 [-], 168	77461823	rubredoxin-type Fe(Cys)4 protein
40	Pfl01_5603	6275924..6276475 [+], 552	77461824	chorismate lyase
41	Pfl01_5604 (ubiA)	6276475..6277365 [+], 891	77461825	4-hydroxybenzoate octaprenyltransferase
42	Pfl01_5605	6277417..6277800 [-], 384	77461826	hypothetical protein
43	Pfl01_5606	6277952..6278641 [+], 690	77461827	two component transcriptional regulator
44	Pfl01_5607	6278680..6280002 [+], 1323	77461828	PAS/PAC sensor Signal transduction histidine kinase
45	Pfl01_5608	6280114..6281454 [+], 1341	77461829	hypothetical protein
46	Pfl01_5609	6281461..6282357 [-], 897	77461830	peptidase M23B

 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) 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