SecReT6
I. Summary
SecReT6 ID40 experimental
StrainPectobacterium atrosepticum SCRI1043
Repliconchromosome [Browse all T6SS(s) in this replicon]
AccessionNC_004547
Location3829218..3869582
CommentVirulence in potato (stem and tuber infection models)
Functionanti-eukaryotic; effector translocation;virulence
T6SS TypeType i; subtype i1
experimental Experimental investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111121111
ComponentTssGTssJTssKTssM
Number1111
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1ECA_RS168453824586..3827465 [-], 2880499407454toprim domain-containing protein 
2ECA_RS168503827578..3827973 [+], 396499407455helix-turn-helix domain-containing protein 
3ECA_RS168553828045..3828374 [+], 330499407456type I toxin-antitoxin system SymE family toxin 
4ECA_RS168603828371..3828715 [+], 345499407461SymE family type I addiction module toxin 
5ECA_RS168653828784..3829215 [-], 432746454807hypothetical protein 
6ECA_RS168703829572..3834074 [-], 4503pseudogeneRHS repeat protein 
7ECA_RS168753834095..3835012 [-], 918499407464DUF4123 domain-containing protein 
8ECA_RS168803835009..3835965 [-], 957499407465DUF4123 domain-containing protein 
9ECA_RS168853836134..3836832 [-], 6991172325015hypothetical protein 
10ECA_RS168903836898..3837596 [-], 699746244844hypothetical protein 
11ECA_RS168953837677..3839050 [-], 1374499407468PAAR domain-containing protein  PAAR
12ECA_RS169003839060..3841096 [-], 2037499407469type VI secretion system tip protein VgrG  TssI
13ECA_RS169053841279..3841797 [-], 519499407470Hcp family type VI secretion system effector  TssD
14ECA_RS169153842363..3843718 [-], 1356499407471sel1 repeat family protein 
15ECA_RS169203843747..3845183 [-], 1437499407472type VI secretion system ImpA family N-terminal domain-containing protein  TssA
16ECA_RS16925 (tssM)3845233..3848730 [-], 3498499407473type VI secretion system membrane subunit TssM  TssM
17ECA_RS16930 (tssA)3848755..3850173 [-], 1419499407474type VI secretion system protein TssA  TssA
18ECA_RS16935 (tagO)3850185..3850745 [-], 561499407475type VI secretion system-associated protein TagO 
19ECA_RS169403850745..3852298 [-], 1554499407476sigma-54-dependent Fis family transcriptional regulator 
20ECA_RS16945 (tssH)3852301..3854898 [-], 2598499407477type VI secretion system ATPase TssH  TssH
21ECA_RS169503854912..3855688 [-], 777499407478type IVB secretion system protein IcmH/DotU  TssL
22ECA_RS16955 (tssK)3855704..3857041 [-], 1338499407479type VI secretion system baseplate subunit TssK  TssK
23ECA_RS16960 (tssJ)3857044..3857565 [-], 522499407480type VI secretion system lipoprotein TssJ  TssJ
24ECA_RS16965 (tagH)3857565..3858785 [-], 1221499407481type VI secretion system-associated FHA domain protein TagH  Fha
25ECA_RS16970 (tssG)3858788..3859786 [-], 999499407482type VI secretion system baseplate subunit TssG  TssG
26ECA_RS16975 (tssF)3859750..3861516 [-], 1767499407483type VI secretion system baseplate subunit TssF  TssF
27ECA_RS16980 (tssE)3861519..3861950 [-], 432499407484type VI secretion system baseplate subunit TssE  TssE
28ECA_RS16985 (tssC)3861956..3863434 [-], 1479499407485type VI secretion system contractile sheath large subunit  TssC
29ECA_RS16990 (tssB)3863466..3863969 [-], 504499407486type VI secretion system contractile sheath small subunit  TssB
30ECA_RS169953865039..3866442 [-], 1404499407487efflux transporter outer membrane subunit 
31ECA_RS170003866439..3869582 [-], 3144499407488multidrug efflux RND transporter permease subunit 
32ECA_RS170053869665..3870837 [-], 1173499407489efflux RND transporter periplasmic adaptor subunit 
33ECA_RS170103871027..3871593 [+], 567499407490TetR/AcrR family transcriptional regulator 
34ECA_RS170153872000..3872545 [-], 546762207304histidine phosphatase family protein 
35ECA_RS170203872983..3873474 [+], 492499407492helix-turn-helix domain-containing protein 
36ECA_RS170253873467..3874063 [+], 597499407493putative adenosine monophosphate-protein transferase Fic 
37ECA_RS235303874068..3874256 [+], 189pseudogenecapsid size determination protein 
38ECA_RS231253874253..3874501 [+], 249499407495ogr/Delta-like zinc finger family protein 
 
flank 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.
 






2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.
 






3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.
 







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 GIProduct  Homolog

Download FASTA format files
Proteins        Genes
N/A
Regulatory element identified
ExpI
RegulatorDescriptionReference
ExpI (ECA0105)Indirect activatorPMID: 18566662

VasH
RegulatorDescriptionReference
VasH (ECA3435)ActivatorPMID: 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] experimental
(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] in_silico
(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] experimental
(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] experimental
 
experimental This literature contains experimental investigation
in_silico This literature contains bioinformatics investigation

Genomics & Bioinformatics Group in MML, SJTU