I. Summary

SecReT6 ID	501
Strain	Pantoea sp. At-9b
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_014837
Location	2727626..2756041
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

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	Pat9b_2499	2722690..2727213 [-], 4524	317048708	YD repeat-containing protein	PAAR
2	Pat9b_2500	2727216..2727629 [-], 414	317048709	hypothetical protein
3	Pat9b_2501	2727626..2729548 [-], 1923	317048710	ImpA family type VI secretion-associated protein	TssI
4	Pat9b_2502	2729569..2731011 [-], 1443	317048711	serine/threonine protein kinase
5	Pat9b_2503	2731041..2733647 [-], 2607	317048712	type VI secretion ATPase, ClpV1 family	TssH
6	Pat9b_2504	2733701..2734750 [-], 1050	317048713	type VI secretion protein	TssG
7	Pat9b_2505	2734747..2736621 [-], 1875	317048714	type VI secretion protein	TssF
8	Pat9b_2506	2736624..2737184 [-], 561	317048715	type VI secretion system lysozyme-like protein	TssE
9	Pat9b_2507	2737174..2738001 [-], 828	317048716	virulence protein SciE type	TagJ
10	Pat9b_2508	2738018..2738977 [-], 960	317048717	hypothetical protein
11	Pat9b_2509	2738988..2739779 [-], 792	317048718	protein serine/threonine phosphatase
12	Pat9b_2510	2739776..2741581 [-], 1806	317048719	FHA domain-containing protein	Fha
13	Pat9b_2511	2741661..2741774 [+], 114	317048720	hypothetical protein
14	Pat9b_2512	2742184..2742579 [-], 396	317048721	hypothetical protein
15	Pat9b_2513	2742635..2743189 [-], 555	317048722	hypothetical protein
16	Pat9b_2514	2743248..2743661 [-], 414	317048723	hypothetical protein
17	Pat9b_2515	2743658..2744650 [-], 993	317048724	hypothetical protein
18	Pat9b_2516	2744761..2745243 [-], 483	317048725	type VI secretion system effector	TssD
19	Pat9b_2517	2745462..2746958 [-], 1497	317048726	type VI secretion protein	TssC
20	Pat9b_2518	2746958..2747488 [-], 531	317048727	type VI secretion protein	TssB
21	Pat9b_2519	2747561..2748571 [-], 1011	317048728	type VI secretion-associated protein	TssA
22	Pat9b_2520	2748584..2749297 [-], 714	317048729	type VI secretion-associated protein
23	Pat9b_2521	2749312..2752938 [-], 3627	317048730	type VI secretion protein IcmF	TssM
24	Pat9b_2522	2752942..2754180 [-], 1239	317048731	DotU family type IV/VI secretion system protein	TssL
25	Pat9b_2523	2754200..2755540 [-], 1341	317048732	type VI secretion protein	TssK
26	Pat9b_2524	2755550..2756041 [-], 492	317048733	type VI secretion lipoprotein	TssJ
27	Pat9b_2525	2756068..2756643 [-], 576	317048734	hypothetical protein
28	Pat9b_2526	2757602..2758258 [-], 657	317048735	binding-protein-dependent transporter inner membrane component
29	Pat9b_2527	2758239..2759339 [-], 1101	317048736	ABC transporter-like protein
30	Pat9b_2528	2759533..2760171 [+], 639	317048737	TetR family transcriptional regulator

 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

SMA2263

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	Pat9b_2516	2744761..2745243 [-], 483	317048725	type VI secretion system effector	SMA2263

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