I. Summary

SecReT6 ID	147
Strain	Rhizobium leguminosarum bv. viciae 3841
Replicon	plasmid pRL12 [Browse all T6SS(s) in this replicon]
Accession	NC_008378
Location	491368..527630
Comment
Function	N/A
T6SS Type	Type i; subtype i5
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	1	1	1	2	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	pRL120452	487612..488223 [-], 612	116249117	putative transmembrane protein
2	pRL120453	488239..490116 [-], 1878	116249118	putative transcriptional regulatory protein
3	pRL120454	490221..490511 [-], 291	116249119	putative transmembrane protein
4	pRL120455	490583..491272 [-], 690	116249120	putative isochorismatase family protein
5	pRL120456	491368..492300 [-], 933	116249121	putative dioxygenase
6	pRL120457	492421..493320 [+], 900	116249122	LysR family transcriptional regulator
7	pRL120458	493557..493889 [-], 333	116249123	hypothetical protein
8	pRL120459	493892..494557 [-], 666	116249124	hypothetical protein
9	pRL120460	494565..494912 [-], 348	116249125	hypothetical protein
10	pRL120461	495175..496314 [+], 1140	116249126	putative capsule polysaccharide export protein
11	pRL120462 (impN)	496311..497225 [-], 915	116249127	putative serine/threonine-protein kinase involved in nitrogen fixation
12	pRL120463 (impM)	497215..498588 [-], 1374	116249128	putative protein involved in nitrogen fixation
13	pRL120464 (impL)	498599..502075 [-], 3477	116249129	ImcF family transmembrane protein involved in nitrogen fixation	TssM
14	pRL120465 (impK)	502072..503604 [-], 1533	116249130	putative outer membrane porin involved in nitrogen fixation	TssL
15	pRL120466 (impJ)	503601..504941 [-], 1341	116249131	hypothetical protein	TssK
16	pRL120467 (impI)	504931..506130 [-], 1200	116249132	FHA domain-containing protein	Fha
17	pRL120468 (impH)	506142..507143 [-], 1002	116249133	hypothetical protein	TssG
18	pRL120469 (impG)	507164..508945 [-], 1782	116249134	hypothetical protein	TssF
19	pRL120470 (impF)	508938..509447 [-], 510	116249135	hypothetical protein	TssE
20	pRL120471 (impE)	509440..510270 [-], 831	116249136	putative virulence-island/protein involved in nitrogen fixation	TagJ
21	pRL120472 (impD)	510267..511655 [-], 1389	116249137	hypothetical protein	TssC
22	pRL120473 (impC)	511731..513212 [-], 1482	116249138	putative virulence-island/protein involved in nitrogen fixation	TssC
23	pRL120474 (impB)	513343..513888 [-], 546	116249139	hypothetical protein	TssB
24	pRL120475 (impA)	513925..514917 [-], 993	116249140	hypothetical protein	TssA
25	pRL120477	517603..518079 [+], 477	116249141	hypothetical protein	TssD
26	pRL120478	518229..519305 [+], 1077	116249142	putative transmembrane protein
27	pRL120479	519351..520244 [+], 894	116249143	hypothetical protein
28	pRL120480	520276..522540 [+], 2265	116249144	putative fimbrial operon related protein	TssI
29	pRL120481	522554..523663 [+], 1110	116249145	hypothetical protein
30	pRL120482	523660..525162 [+], 1503	116249146	hypothetical protein
31	pRL120483	525159..526274 [+], 1116	116249147	hypothetical protein
32	pRL120484	526530..527630 [+], 1101	116249148	hypothetical protein
33	pRL120485	527666..528412 [+], 747	116249149	hypothetical protein
34	pRL120486	528409..529587 [+], 1179	116249150	hypothetical protein
35	pRL120487	529643..531088 [-], 1446	116249151	putative salicylaldehyde dehydrogenase
36	pRL120488	531112..531915 [-], 804	116249152	3-alpha-hydroxysteroid dehydrogenase

 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

Atu4345 , RbsB

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	pRL120477	517603..518079 [+], 477	116249141	hypothetical protein	Atu4345
2	RL2721(rbsB)	2879719..2880648 [+], 930	116252468	D-ribose-binding protein component of ABC transporter	RbsB

Download FASTA format files

Proteins        Genes

N/A

(1) 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