I. Summary

SecReT6 ID	387
Strain	Erwinia amylovora CFBP1430
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_013961
Location	3291637..3325348
Comment
Function	N/A
T6SS Type	Type i; subtype i2
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	4	2	1	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	2	1	1

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	EAMY_3197 (nikS)	3288300..3289466 [-], 1167	292489660	carbamoyl-phosphate synthase large subunit
2	EAMY_3198	3290401..3290670 [-], 270	292489661	hypothetical protein
3	EAMY_3199	3291119..3291307 [-], 189	292489662	plasmid-like protein
4	EAMY_3200	3291366..3291587 [-], 222	292489663	hypothetical protein
5	EAMY_3201	3291637..3293037 [-], 1401	292489664	type VI secretion system core protein	TssA
6	EAMY_3202	3293082..3293534 [-], 453	292489665	type VI secretion system core protein	TssE
7	EAMY_3203	3294088..3294261 [+], 174	292489666	hypothetical protein
8	EAMY_3204	3294266..3295156 [-], 891	292489667	hypothetical protein	TssI
9	EAMY_3205	3295172..3295267 [+], 96	292489668	hypothetical protein
10	EAMY_3206	3295981..3296565 [-], 585	292489669	hypothetical protein	TssI
11	EAMY_3207	3296570..3296995 [-], 426	292489670	hypothetical protein	TssJ
12	EAMY_3208	3297099..3297842 [-], 744	292489671	hypothetical protein
13	EAMY_3209	3299044..3299826 [-], 783	292489672	hypothetical protein
14	EAMY_3210	3299826..3300380 [-], 555	292489673	hypothetical protein
15	EAMY_3211	3300382..3302694 [-], 2313	292489674	type VI secretion system effector protein VgrG	TssI
16	EAMY_3212	3302699..3303223 [-], 525	292489675	type VI secretion system core protein	TssJ
17	EAMY_3213	3303249..3304331 [-], 1083	292489676	type VI secretion system core protein	TssG
18	EAMY_3214	3304295..3306064 [-], 1770	292489677	type VI secretion system core protein	TssF
19	EAMY_3215	3306219..3307826 [-], 1608	292489678	type VI secretion system core protein	TssA
20	EAMY_3216	3307823..3311194 [-], 3372	292489679	type VI secretion system core protein	TssM
21	EAMY_3217	3311187..3312395 [-], 1209	292489680	hypothetical protein
22	EAMY_3218	3312398..3312667 [-], 270	292489681	hypothetical protein	PAAR
23	EAMY_3219	3312806..3313345 [-], 540	292489682	hypothetical protein
24	EAMY_3220	3313420..3315777 [-], 2358	292489683	type VI secretion system effector protein VgrG	TssI
25	EAMY_3221	3315923..3316132 [-], 210	292489684	hypothetical protein
26	EAMY_3222 (clpV3)	3316218..3318878 [-], 2661	292489685	type VI secretion system core protein ATPase	TssH
27	EAMY_3223 (hcp)	3319049..3319540 [-], 492	292489686	type VI secretion system effector protein hcp	TssD
28	EAMY_3224	3319573..3321228 [-], 1656	292489687	type VI secretion system-associated protein	TagL
29	EAMY_3225	3321228..3321905 [-], 678	292489688	type VI secretion system-associated protein	TssL
30	EAMY_3226	3321902..3323251 [-], 1350	292489689	type VI secretion system core protein	TssK
31	EAMY_3227	3323269..3324816 [-], 1548	292489690	type VI secretion system core protein	TssC
32	EAMY_3228	3324851..3325348 [-], 498	292489691	type VI secretion system core protein	TssB
33	EAMY_3229	3325818..3325997 [+], 180	292489692	hypothetical protein
34	EAMY_3230	3325977..3326078 [-], 102	292489693	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

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

EC042_4529

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	EAMY_3223(hcp)	3319049..3319540 [-], 492	292489686	type VI secretion system effector protein hcp	EC042_4529

Download FASTA format files

Proteins        Genes

N/A

(1) Mann RA et al. (2013). Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. PLoS One. 8(2):e55644. [PudMed:23409014]

(2) 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