Detailed information of T6SS
Note: only experimentally validated proteins are displayed in the graph.
Summary
| T6SS ID | T6SS00035  |
| T6SS type | Type i3 |
| Strain | Pseudomonas protegens Pf-5 |
| Replicon (RefSeq) | chromosome (NC_004129) |
| Location | 6897920..6930515 |
| Function | anti-bacterial; effector translocation |
| Comment | T6-secretion of a peptidoglycan amidase enzyme (antibacterial activity of T6SS implied). |
| References | [1] Whitney JC et al (2013) Identification, structure and function of a novel type VI secretion peptidoglycan glycoside hydrolase effector-immunity pair. J Biol Chem. 288(37):26616-24. [PudMed:23878199] [2] Hassan KA et al (2010) Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences. Environ Microbiol. 12(4):899-915. [PudMed:20089046] [3] Loper JE et al (2012) Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions. PLoS Genet. 8(7):e1002784. [PudMed:22792073] [4] Barret M et al (2011) Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. Microbiology. 157(Pt 6):1726-39. [PudMed:21474537] [5] Russell AB et al (2012) A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host Microbe. 11(5):538-49. [PudMed:22607806] |
Experimental investigation has been performed.T6SS components and genome coordinates
| Component | FHA | PAAR | PpkA | PppA | TagF | TagQ | TagR | TagS | TagT | TssA | TssB | TssC | TssD | TssE | TssF | TssG | TssH | TssI | TssJ | TssK | TssL | TssM |
| Number | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 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 |
|---|---|---|---|---|---|---|---|
| PFL_RS30780 | 6893219..6894619 | + | 1401 | WP_011064240.1 | HDOD domain-containing protein | ||
| PFL_RS30785 | 6894678..6895061 | - | 384 | WP_015637475.1 | hypothetical protein | ||
| T6CP012428 | TagQ | PFL_RS30790 | 6895202..6896131 | - | 930 | WP_011064242.1 | hypothetical protein |
| T6CP012430 | TagR | PFL_RS30795 | 6896215..6897927 | - | 1713 | WP_011064243.1 | SUMF1/EgtB/PvdO family nonheme iron enzyme |
| T6CP012431 | TagS | PFL_RS30800 | 6897920..6899122 | - | 1203 | WP_011064244.1 | ABC transporter permease |
| T6CP012432 | TagT | PFL_RS30805 | 6899122..6899838 | - | 717 | WP_011064245.1 | ABC transporter ATP-binding protein |
| T6CP012429 | PpkA | PFL_RS30810 | 6899838..6902921 | - | 3084 | WP_011064246.1 | serine/threonine-protein kinase |
| T6CP012433 | PppA | PFL_RS30815 | 6902924..6903658 | - | 735 | WP_011064247.1 | protein phosphatase 2C domain-containing protein |
| T6CP012434 | TagF | PFL_RS30820 (tagF) | 6903659..6904312 | - | 654 | WP_011064248.1 | type VI secretion system-associated protein TagF |
| T6CP000275 | TssM | PFL_RS30825 (tssM) | 6904309..6907815 | - | 3507 | WP_011064249.1 | type VI secretion system membrane subunit TssM |
| T6CP000276 | TssL | PFL_RS30830 | 6907812..6909137 | - | 1326 | WP_011064250.1 | DotU family type VI secretion system protein |
| T6CP000277 | TssK | PFL_RS30835 (tssK) | 6909144..6910478 | - | 1335 | WP_011064251.1 | type VI secretion system baseplate subunit TssK |
| T6CP000278 | TssJ | PFL_RS30840 (tssJ) | 6910494..6911000 | - | 507 | WP_011064252.1 | type VI secretion system lipoprotein TssJ |
| T6CP011428 | FHA | PFL_RS30845 (tagH) | 6911065..6912549 | - | 1485 | WP_011064253.1 | type VI secretion system-associated FHA domain protein TagH |
| T6CP000279 | TssA | PFL_RS30850 (tssA) | 6912942..6913961 | + | 1020 | WP_011064254.1 | type VI secretion system protein TssA |
| T6CP000280 | TssB | PFL_RS30855 (tssB) | 6914043..6914558 | + | 516 | WP_011064255.1 | type VI secretion system contractile sheath small subunit |
| T6CP000281 | TssC | PFL_RS30860 (tssC) | 6914575..6916068 | + | 1494 | WP_011064256.1 | type VI secretion system contractile sheath large subunit |
| T6CP000282 | TssD | PFL_RS30865 | 6916187..6916675 | + | 489 | WP_011064257.1 | type VI secretion system tube protein Hcp |
| T6CP000283 | TssE | PFL_RS30870 (tssE) | 6916836..6917351 | + | 516 | WP_011064258.1 | type VI secretion system baseplate subunit TssE |
| T6CP000284 | TssF | PFL_RS30875 (tssF) | 6917348..6919207 | + | 1860 | WP_011064259.1 | type VI secretion system baseplate subunit TssF |
| T6CP000285 | TssG | PFL_RS30880 (tssG) | 6919171..6920223 | + | 1053 | WP_011064260.1 | type VI secretion system baseplate subunit TssG |
| T6CP000286 | TssH | PFL_RS30885 (tssH) | 6920216..6922891 | + | 2676 | WP_011064261.1 | type VI secretion system ATPase TssH |
| T6CP000287 | TssI | PFL_RS30890 | 6923022..6924959 | + | 1938 | WP_011064262.1 | type VI secretion system tip protein VgrG |
| PFL_RS30895 | 6924978..6925403 | + | 426 | WP_011064263.1 | DUF1795 domain-containing protein | ||
| T6CP011355 | PAAR | PFL_RS30900 | 6925413..6929873 | + | 4461 | WP_011064264.1 | RHS domain-containing protein |
| PFL_RS30905 | 6929889..6930515 | + | 627 | WP_011064265.1 | hypothetical protein | ||
| PFL_RS30910 | 6930535..6930798 | - | 264 | WP_041120412.1 | hypothetical protein | ||
| PFL_RS30915 | 6930853..6931287 | - | 435 | WP_011064267.1 | DcrB-related protein | ||
| PFL_RS30920 | 6931399..6931770 | - | 372 | WP_041120416.1 | hypothetical protein | ||
| PFL_RS30925 | 6931758..6932282 | - | 525 | WP_019093146.1 | hypothetical protein | ||
| PFL_RS30930 | 6932447..6932722 | - | 276 | WP_011064269.1 | HU family DNA-binding protein | ||
| PFL_RS30935 | 6932912..6934060 | - | 1149 | WP_011064270.1 | FAD-dependent oxidoreductase | ||
| PFL_RS30940 | 6934103..6934270 | - | 168 | WP_011064271.1 | rubredoxin | ||
| PFL_RS30945 | 6934486..6935049 | + | 564 | WP_011064272.1 | chorismate lyase |
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) |
|---|---|---|---|---|---|---|---|---|
| REG0091 |
PFL_RS17995 (gacA/uvrY/SirA) | protein | TCS-RR | Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 4110513..4111154 (-) | 499374263 | T6SS transcripts (↓) |
| REG0092 |
PFL_RS30815 (pppA) | protein | Tpp | Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 6902924..6903658 (-) | 499376669 | Hcp secretion (↑) |
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 |
|---|---|---|---|---|---|---|---|
| EFF01474 |
PFL_6096 (rhsA) | Tde | IMU00300 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 6925413..6929873 (+) | 68347678 |
| EFF00045 |
PFL_5498 (Tae3) | Tae | IMU00073 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 6278373..6278744 (+) | 70732799 |
| EFF00434 |
PFL_3037 (Tge2) | Tge | IMU00074 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 3502760..3503293 (-) | 70730402 |
| EFF01475 |
PFL_6209 (Tne2) | Tne | IMU00301 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 7049182..7050408 (+) | 68347791 |
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 |
|---|---|---|---|---|---|---|
| IMU00073 |
PFL_5499 (Tai3) | EFF00045 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 6278755..6279204 (+) | 70732800 |
| IMU00074 |
PFL_3036 (Tgi2) | EFF00434 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 3502296..3502766 (-) | 70730401 |
| IMU00300 |
PFL_6097 (rhsI) | EFF01474 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 6929889..6930515 (+) | 70733380 |
| IMU00301 |
PFL_6210 (Tni2) | EFF01475 |
Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 7050414..7050875 (+) | 70733493 |
Experimental investigation has been performed.| Accessory protein ID | Locus tag (Gene) | Type | Organism | Replicon (Accession) | Coordinates (Strand) | NCBI ID | Related structure protein | Related effector |
|---|---|---|---|---|---|---|---|---|
| ACP00012 |
PFL_6095 (eagR1) | adaptor | Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 6924978..6925403 (+) | 499376685 | - | PFL_6096 (RhsA) |
| ACP00013 |
PFL_6099 (eagT2) | adaptor | Pseudomonas protegens Pf-5 | chromosome (NC_004129) | 6930853..6931287 (-) | 499376689 | - | PFL_6209 (Tne2) |