I. Summary

SecReT6 ID	146
Strain	Shewanella frigidimarina NCIMB 400
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_008345
Location	2809539..2832266
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	1	1	1	1	1	1	2	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	Sfri_2356	2806787..2807731 [-], 945	114563526	hypothetical protein
2	Sfri_2357	2807728..2808828 [-], 1101	114563527	hypothetical protein
3	Sfri_2358	2808850..2809140 [-], 291	114563528	PAAR repeat-containing protein	PAAR
4	Sfri_2359	2809183..2809536 [-], 354	114563529	hypothetical protein
5	Sfri_2360	2809539..2811395 [-], 1857	114563530	Rhs element Vgr protein	TssI
6	Sfri_2361	2811466..2811945 [-], 480	114563531	hypothetical protein	TssD
7	Sfri_2362	2812315..2814921 [-], 2607	114563532	ATPase	TssH
8	Sfri_2363	2814941..2815948 [-], 1008	114563533	hypothetical protein	TssG
9	Sfri_2364	2815945..2817774 [-], 1830	114563534	hypothetical protein	TssF
10	Sfri_2365	2817771..2818235 [-], 465	114563535	hypothetical protein	TssE
11	Sfri_2366	2818268..2819056 [-], 789	114563536	virulence protein, SciE type	TagJ
12	Sfri_2367	2819071..2820606 [-], 1536	114563537	hypothetical protein	TssC
13	Sfri_2368	2820658..2822151 [-], 1494	114563538	hypothetical protein	TssC
14	Sfri_2369	2822151..2822651 [-], 501	114563539	hypothetical protein	TssB
15	Sfri_2370	2822693..2823799 [-], 1107	114563540	ImpA domain-containing protein	TssA
16	Sfri_2371	2824086..2824853 [-], 768	114563541	protein serine/threonine phosphatase
17	Sfri_2372	2824844..2825575 [-], 732	114563542	hypothetical protein
18	Sfri_2373	2825557..2829105 [-], 3549	114563543	ImcF domain-containing protein	TssM
19	Sfri_2374	2829129..2830418 [-], 1290	114563544	OmpA/MotB domain-containing protein	TssL
20	Sfri_2375	2830443..2831771 [-], 1329	114563545	hypothetical protein	TssK
21	Sfri_2376	2831796..2832266 [-], 471	114563546	hypothetical protein	TssJ
22	Sfri_2377	2832285..2833661 [-], 1377	114563547	FHA domain-containing protein	Fha
23	Sfri_2378	2833694..2835679 [-], 1986	114563548	serine/threonine protein kinase
24	Sfri_2379	2835999..2836490 [+], 492	114563549	OmpA/MotB domain-containing protein	TagL

 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

VPA1027

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	Sfri_2361	2811466..2811945 [-], 480	114563531	hypothetical protein	VPA1027

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