Detailed information of T6SS
Note: only experimentally validated proteins are displayed in the graph.
Summary
| T6SS ID | T6SS00040  |
| T6SS type | Type i1 |
| Strain | Pectobacterium atrosepticum SCRI1043 |
| Replicon (RefSeq) | chromosome (NC_004547) |
| Location | 3829218..3869582 |
| Function | anti-eukaryotic; effector translocation; virulence |
| Comment | Virulence in potato (stem and tuber infection models). |
| References | [1] 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] [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. 0.488888889. [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] 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] [5] 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 investigation has been performed.T6SS components and genome coordinates
| Component | FHA | PAAR | TssA | TssB | TssC | TssD | TssE | TssF | TssG | TssH | TssI | TssJ | TssK | TssL | TssM |
| Number | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Component ID | Component | Locus tag (Gene) | Coordinate | Strand | Size (bp) | NCBI ID | Product |
|---|---|---|---|---|---|---|---|
| ECA_RS16845 | 3824586..3827465 | - | 2880 | WP_011094921.1 | toprim domain-containing protein | ||
| ECA_RS16850 | 3827578..3827973 | + | 396 | WP_011094922.1 | helix-turn-helix domain-containing protein | ||
| ECA_RS16855 | 3828045..3828374 | + | 330 | WP_011094923.1 | type I toxin-antitoxin system SymE family toxin | ||
| ECA_RS16860 | 3828371..3828715 | + | 345 | WP_011094928.1 | SymE family type I addiction module toxin | ||
| ECA_RS16865 | 3828784..3829215 | - | 432 | WP_039494437.1 | hypothetical protein | ||
| ECA_RS16870 | 3829572..3834074 | - | 4503 | pseudogene | RHS repeat protein | ||
| ECA_RS16875 | 3834095..3835012 | - | 918 | WP_011094931.1 | DUF4123 domain-containing protein | ||
| ECA_RS16880 | 3835009..3835965 | - | 957 | WP_011094932.1 | DUF4123 domain-containing protein | ||
| ECA_RS16885 | 3836134..3836832 | - | 699 | WP_080708294.1 | hypothetical protein | ||
| ECA_RS16890 | 3836898..3837596 | - | 699 | WP_039293252.1 | hypothetical protein | ||
| T6CP011433 | PAAR | ECA_RS16895 | 3837677..3839050 | - | 1374 | WP_011094935.1 | PAAR domain-containing protein |
| T6CP008452 | TssI | ECA_RS16900 | 3839060..3841096 | - | 2037 | WP_011094936.1 | type VI secretion system tip protein VgrG |
| T6CP008453 | TssD | ECA_RS16905 | 3841279..3841797 | - | 519 | WP_011094937.1 | Hcp family type VI secretion system effector |
| ECA_RS16915 | 3842363..3843718 | - | 1356 | WP_011094938.1 | sel1 repeat family protein | ||
| T6CP008454 | TssA | ECA_RS16920 | 3843747..3845183 | - | 1437 | WP_011094939.1 | type VI secretion system ImpA family N-terminal domain-containing protein |
| T6CP008455 | TssM | ECA_RS16925 (tssM) | 3845233..3848730 | - | 3498 | WP_011094940.1 | type VI secretion system membrane subunit TssM |
| T6CP008456 | TssA | ECA_RS16930 (tssA) | 3848755..3850173 | - | 1419 | WP_011094941.1 | type VI secretion system protein TssA |
| ECA_RS16935 (tagO) | 3850185..3850745 | - | 561 | WP_011094942.1 | type VI secretion system-associated protein TagO | ||
| ECA_RS16940 | 3850745..3852298 | - | 1554 | WP_011094943.1 | sigma-54 dependent transcriptional regulator | ||
| T6CP008457 | TssH | ECA_RS16945 (tssH) | 3852301..3854898 | - | 2598 | WP_011094944.1 | type VI secretion system ATPase TssH |
| T6CP000327 | TssL | ECA_RS16950 | 3854912..3855688 | - | 777 | WP_011094945.1 | type IVB secretion system protein IcmH/DotU |
| T6CP000328 | TssK | ECA_RS16955 (tssK) | 3855704..3857041 | - | 1338 | WP_011094946.1 | type VI secretion system baseplate subunit TssK |
| T6CP000329 | TssJ | ECA_RS16960 (tssJ) | 3857044..3857565 | - | 522 | WP_011094947.1 | type VI secretion system lipoprotein TssJ |
| T6CP011432 | FHA | ECA_RS16965 (tagH) | 3857565..3858785 | - | 1221 | WP_011094948.1 | type VI secretion system-associated FHA domain protein TagH |
| T6CP000330 | TssG | ECA_RS16970 (tssG) | 3858788..3859786 | - | 999 | WP_011094949.1 | type VI secretion system baseplate subunit TssG |
| T6CP000331 | TssF | ECA_RS16975 (tssF) | 3859750..3861516 | - | 1767 | WP_011094950.1 | type VI secretion system baseplate subunit TssF |
| T6CP008458 | TssE | ECA_RS16980 (tssE) | 3861519..3861950 | - | 432 | WP_011094951.1 | type VI secretion system baseplate subunit TssE |
| T6CP000332 | TssC | ECA_RS16985 (tssC) | 3861956..3863434 | - | 1479 | WP_011094952.1 | type VI secretion system contractile sheath large subunit |
| T6CP000333 | TssB | ECA_RS16990 (tssB) | 3863466..3863969 | - | 504 | WP_011094953.1 | type VI secretion system contractile sheath small subunit |
| ECA_RS16995 | 3865039..3866442 | - | 1404 | WP_011094954.1 | efflux transporter outer membrane subunit | ||
| ECA_RS17000 | 3866439..3869582 | - | 3144 | WP_011094955.1 | multidrug efflux RND transporter permease subunit | ||
| ECA_RS17005 | 3869665..3870837 | - | 1173 | WP_011094956.1 | efflux RND transporter periplasmic adaptor subunit | ||
| ECA_RS17010 | 3871027..3871593 | + | 567 | WP_011094957.1 | TetR/AcrR family transcriptional regulator | ||
| ECA_RS17015 | 3872000..3872545 | - | 546 | WP_043878086.1 | phosphoglycerate mutase family protein | ||
| ECA_RS17020 | 3872983..3873474 | + | 492 | WP_011094959.1 | YhfG family protein | ||
| ECA_RS17025 | 3873467..3874063 | + | 597 | WP_011094960.1 | putative adenosine monophosphate-protein transferase Fic | ||
| ECA_RS23530 | 3874068..3874256 | + | 189 | pseudogene | capsid size determination protein | ||
| ECA_RS23125 | 3874253..3874501 | + | 249 | WP_011094962.1 | ogr/Delta-like zinc finger family protein |
Genes in the 5-Kb flanking regions if available, or non-core components encoded by the T6SS gene cluster if any.
Download FASTA format files
Note: in the 'Target' column, ↓ means the target is positively regulated by the regulator, while ↑ indicates negatively regulation.
Experimental investigation has been performed.
Bioinformatics investigation has been performed.| Regulator ID | Locus tag (Gene) | Regulator type | Regulatory pathway | Organism | Replicon (Accession) | Coordinates (Strand) | NCBI ID | Target (Regulation) |
|---|---|---|---|---|---|---|---|---|
| REG0093 |
ECA_RS00520 (expI) | protein | QS regulatory pathway | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 125689..126339 (+) | 499404281 | T6SS transcripts (ECA4275[hcp1], ECA3428[hcp2] and ECA2866[hcp3]) (↓) |
| REG0094 |
ECA3435 (bEBP/VasH) | protein | Global regulator | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 3850745..3852298 (-) | 499407476 | T6SS gene cluster promoter (PECA3445) (↓); Hcp gene cluster promoter (PECA4275) (↓); Hcp gene cluster promoter (PECA2866) (↓) |
| REG0095 |
ECA0288 (rpoN) | protein | Global regulator | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 336007..337440 (-) | 499404454 | T6SS gene cluster promoter (PECA3445) (↓); Hcp gene cluster promoter (PECA4275) (↓); Hcp gene cluster promoter (PECA2866) (↓) |
Experimental investigation has been performed. Bioinformatics investigation has been performed.| Effector ID | Locus tag (Gene) | Classification | Cognate immunity protein | Organism | Replicon (Accession) | Coordinates (Strand) | NCBI ID |
|---|---|---|---|---|---|---|---|
| EFF00055 |
ECA_RS21185 | - | - | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 4790053..4790571 (+) | 50123195 |
| EFF00050 |
ECA_RS02315 | - | - | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 520562..521041 (-) | 50119407 |
| EFF00051 |
ECA_RS14065 | - | - | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 3204842..3205360 (+) | 50121790 |
| EFF00053 |
ECA_RS16900 | - | - | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 3839060..3841096 (-) | 50122351 |
| EFF00054 |
ECA_RS16905 | - | - | Pectobacterium atrosepticum SCRI1043 | chromosome (NC_004547) | 3841279..3841797 (-) | 50122352 |
Experimental investigation has been performed. Bioinformatics investigation has been performed.| Immunity protein ID | Locus tag (Gene) | Cognate effector | Organism | Replicon (Accession) | Coordinates (Strand) | NCBI ID |
|---|
Experimental investigation has been performed.| Accessory protein ID | Locus tag (Gene) | Type | Organism | Replicon (Accession) | Coordinates (Strand) | NCBI ID | Related structure protein | Related effector |
|---|