I. Summary

SecReT6 ID	40
Strain	Pectobacterium atrosepticum SCRI1043
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_004547
Location	3829218..3869582
Comment	Virulence in potato (stem and tuber infection models)
Function	anti-eukaryotic; effector translocation;virulence
T6SS Type	Type i; subtype i1
Experimental 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	2	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	ECA3416	3824586..3827465 [-], 2880	50122340	DnaG primase-like protein
2	ECA3417	3827578..3827973 [+], 396	50122341	phage regulatory protein
3	ECA3418	3828045..3828374 [+], 330	50122342	hypothetical protein
4	ECA3419	3828371..3828715 [+], 345	50122343	hypothetical protein
5	ECA3420	3828784..3829221 [-], 438	50122344	hypothetical protein
6	ECA3421	3829218..3834074 [-], 4857	50122345	Rhs protein
7	ECA3422	3834095..3835012 [-], 918	50122346	hypothetical protein
8	ECA3423	3835009..3835965 [-], 957	50122347	hypothetical protein
9	ECA3424	3836134..3836901 [-], 768	50122348	lipoprotein
10	ECA3425	3836898..3837677 [-], 780	50122349	lipoprotein
11	ECA3426	3837677..3839050 [-], 1374	50122350	phospholipase	PAAR
12	ECA3427	3839060..3841096 [-], 2037	50122351	hypothetical protein	TssI
13	ECA3428	3841279..3841797 [-], 519	50122352	hypothetical protein	TssD
14	ECA3430	3842363..3843718 [-], 1356	50122353	lipoprotein
15	ECA3431	3843747..3845183 [-], 1437	50122354	hypothetical protein	TssA
16	ECA3432	3845233..3848730 [-], 3498	50122355	virulence-associated protein	TssM
17	ECA3433	3848755..3850173 [-], 1419	50122356	hypothetical protein	TssA
18	ECA3434	3850185..3850745 [-], 561	50122357	hypothetical protein
19	ECA3435	3850745..3852298 [-], 1554	50122358	sigma-54 dependent transcriptional regulator
20	ECA3436	3852301..3854898 [-], 2598	50122359	chaperone	TssH
21	ECA3437	3854912..3855688 [-], 777	50122360	hypothetical protein	TssL
22	ECA3438	3855704..3857041 [-], 1338	50122361	hypothetical protein	TssK
23	ECA3439	3857044..3857565 [-], 522	50122362	lipoprotein	TssJ
24	ECA3440	3857565..3858785 [-], 1221	50122363	hypothetical protein	Fha
25	ECA3441	3858788..3859786 [-], 999	50122364	hypothetical protein	TssG
26	ECA3442	3859750..3861516 [-], 1767	50122365	hypothetical protein	TssF
27	ECA3443	3861519..3861950 [-], 432	50122366	hypothetical protein	TssE
28	ECA3444	3861956..3863434 [-], 1479	50122367	hypothetical protein	TssC
29	ECA3445	3863466..3863969 [-], 504	50122368	hypothetical protein	TssB
30	ECA3446 (oprJ)	3865039..3866442 [-], 1404	50122369	multidrug resistance outer membrane protein
31	ECA3447 (mexB)	3866439..3869582 [-], 3144	50122370	multidrug resistance protein
32	ECA3448 (mexC)	3869665..3870837 [-], 1173	50122371	multidrug resistance protein
33	ECA3449 (nfxB)	3871027..3871593 [+], 567	50122372	transcriptional regulator
34	ECA3450	3872000..3872587 [-], 588	50122373	hypothetical protein
35	ECA3451	3872983..3873474 [+], 492	50122374	hypothetical protein
36	ECA3452 (fic)	3873467..3874063 [+], 597	50122375	cell filamentation protein
37	ECA3453	3874071..3874256 [+], 186	50122376	phage capsid protein (partial)
38	ECA3454	3874253..3874501 [+], 249	50122377	bacteriophage regulatory 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

ECA0456 , ABG57133, ECA2866, ECA3427, Dda3937_02773, ECA3427, ECA3428, ABG57133, ECA4275, ECA3427, Dda3937_02773

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	ECA0456	520562..521041 [-], 480	50119407	hypothetical protein	ECA0456
2	ECA2104	2390748..2392775 [+], 2028	50121032	VgrG protein	ABG57133
3	ECA2866	3204842..3205360 [+], 519	50121790	hypothetical protein	ECA2866
4	ECA2867(vgrG)	3205452..3207311 [+], 1860	50121791	RHS accessory genetic element	ECA3427
5	ECA2869(rhs)	3207776..3212035 [+], 4260	50121793	RHS protein	Dda3937_02773
6	ECA3427	3839060..3841096 [-], 2037	50122351	hypothetical protein	ECA3427
7	ECA3428	3841279..3841797 [-], 519	50122352	hypothetical protein	ECA3428
8	ECA4142	4624416..4626443 [+], 2028	50123062	RHS accessory genetic element	ABG57133
9	ECA4275	4790053..4790571 [+], 519	50123195	hypothetical protein	ECA4275
10	ECA4276	4790693..4792522 [+], 1830	50123196	Rhs-family protein	ECA3427
11	ECA4278	4792990..4797273 [+], 4284	50123198	Rhs-family protein	Dda3937_02773
Data from experimental literature

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Proteins        Genes

N/A

Regulatory element identified

ExpI

Regulator	Description	Reference
ExpI (ECA0105)	Indirect activator	PMID: 18566662

VasH

Regulator	Description	Reference
VasH (ECA3435)	Activator	PMID: 21378190

(1) Bernard CS et al. (2011). Regulation of type VI secretion gene clusters by sigma54 and cognate enhancer binding proteins. J Bacteriol. 193(9):2158-67. [PudMed:21378190]

(2) 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]

(3) Mattinen L et al. (2008). Microarray profiling of host-extract-induced genes and characterization of the type VI secretion cluster in the potato pathogen Pectobacterium atrosepticum. Microbiology. 154(Pt 8):2387-96. [PudMed:18667571]

(4) Liu H et al. (2008). Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum. PLoS Pathog. 4(6):e1000093. [PudMed:18566662]

(5) Mattinen L et al. (2007). Host-extract induced changes in the secretome of the plant pathogenic bacterium Pectobacterium atrosepticum. Proteomics. 7(19):3527-37. [PudMed:17726675]

This literature contains experimental investigation

This literature contains bioinformatics investigation