I. Summary

SecReT6 ID	411
Strain	Pantoea vagans C9-1
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_014562
Location	1073370..1102136
Comment
Function	N/A
T6SS Type	Type i; subtype i3
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	1	1	1

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III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	Pvag_1018 (guaa1)	1068653..1069378 [+], 726	308186529	GMP synthase
2	Pvag_1019	1069366..1069929 [-], 564	308186530	trans-aconitate 2-methyltransferase
3	Pvag_1020 (aldB)	1070163..1071683 [+], 1521	308186531	aldehyde dehydrogenase
4	Pvag_1021	1072750..1073346 [+], 597	308186532	type VI secretion system-associated hypothetical protein
5	Pvag_1022	1073370..1073867 [+], 498	308186533	type VI secretion system, core protein	TssJ
6	Pvag_1023	1073873..1075213 [+], 1341	308186534	type VI secretion system, core protein	TssK
7	Pvag_1024	1075231..1076469 [+], 1239	308186535	type VI secretion system, core protein	TssL
8	Pvag_1025	1076473..1080102 [+], 3630	308186536	type VI secretion system, core protein	TssM
9	Pvag_1026	1080117..1080833 [+], 717	308186537	type VI secretion system-associated hypothetical protein
10	Pvag_1027	1080844..1081866 [+], 1023	308186538	type VI secretion system, core protein	TssA
11	Pvag_1028	1081946..1082479 [+], 534	308186539	type VI secretion system, core protein	TssB
12	Pvag_1029	1082476..1083975 [+], 1500	308186540	type VI secretion system, core protein	TssC
13	Pvag_1030	1084021..1084281 [+], 261	308186541	hypothetical protein
14	Pvag_1031 (hcp)	1084523..1085005 [+], 483	308186542	type VI secretion system, effector protein hcp	TssD
15	Pvag_1032	1085110..1086102 [+], 993	308186543	type VI secretion system-associated hypothetical protein
16	Pvag_1033	1086655..1087038 [+], 384	308186544	type VI secretion system-associated hypothetical protein
17	Pvag_1034	1086992..1087450 [+], 459	308186545	type VI secretion system-associated hypothetical protein
18	Pvag_1035	1087748..1089607 [+], 1860	308186546	type VI secretion system, core protein	Fha
19	Pvag_1036	1089604..1090395 [+], 792	308186547	type VI secretion system, Serine/threonine protein phosphatase
20	Pvag_1037	1090322..1091383 [+], 1062	308186548	type VI secretion system-associated hypothetical protein
21	Pvag_1038	1091400..1092227 [+], 828	308186549	type VI secretion system-associated hypothetical protein	TagJ
22	Pvag_1039	1092217..1092792 [+], 576	308186550	type VI secretion system, core protein	TssE
23	Pvag_1040	1092795..1094666 [+], 1872	308186551	type VI secretion system, core protein	TssF
24	Pvag_1041	1094525..1095709 [+], 1185	308186552	type VI secretion system, core protein	TssG
25	Pvag_1042 (clpV)	1095764..1098373 [+], 2610	308186553	type VI secretion system, core protein ATPase	TssH
26	Pvag_1043	1098401..1099903 [+], 1503	308186554	type VI secretion system, serine- threonine protein kinase
27	Pvag_1044 (vgrS)	1099920..1102136 [+], 2217	308186555	type VI secretion system, effector protein vgrS	TssI
28	Pvag_1045	1102497..1103285 [+], 789	308186556	hypothetical protein
29	Pvag_1046	1104441..1105286 [+], 846	308186557	hypothetical protein
30	Pvag_1047	1105367..1105744 [+], 378	308186558	hypothetical 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

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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

SMA2263 , ECL_01567

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	Pvag_1031(hcp)	1084523..1085005 [+], 483	308186542	type VI secretion system, effector protein hcp	SMA2263
2	Pvag_1048(rhs)	1105748..1110229 [+], 4482	308186559	Rhs-family protein	ECL_01567

Download FASTA format files

Proteins        Genes

N/A

(1) De Maayer P et al. (2011). Comparative genomics of the Type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins. BMC Genomics. 12:576. [PudMed:22115407]

This literature contains bioinformatics investigation