Detailed information of T6SS
Note: only experimentally validated proteins are displayed in the graph.
Summary
| T6SS ID | T6SS00014  |
| T6SS type | Type i4b |
| Strain | Pseudomonas putida KT2440 |
| Replicon (RefSeq) | chromosome (NC_002947) |
| Location | 3470069..3499780 |
| Function | anti-bacterial |
| Comment | The K1-T6SS is anti-bacterial and can secrete HCP1. |
| References | [1] Bernal P, Allsopp LP, Filloux A, Llamas MA. et al (2017) The Pseudomonas putida T6SS is a plant warden against phytopathogens.. ISME J. 11(4):972-987. [PudMed:28045455] [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] 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] |
Experimental investigation has been performed.T6SS components and genome coordinates
| Component | 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 | 2 |
| Component ID | Component | Locus tag (Gene) | Coordinate | Strand | Size (bp) | NCBI ID | Product |
|---|---|---|---|---|---|---|---|
| PP_RS15950 | 3466349..3466900 | - | 552 | WP_049586097.1 | YbhB/YbcL family Raf kinase inhibitor-like protein | ||
| PP_RS15955 | 3466949..3467257 | - | 309 | WP_019438461.1 | hypothetical protein | ||
| PP_RS15960 | 3467339..3468637 | - | 1299 | WP_020190937.1 | MFS transporter | ||
| PP_RS15965 | 3469064..3469939 | + | 876 | WP_010953981.1 | AEC family transporter | ||
| PP_RS15970 | 3470072..3472489 | - | 2418 | WP_049586093.1 | TonB-dependent receptor | ||
| PP_RS15975 | 3472639..3473601 | - | 963 | WP_049586091.1 | FecR domain-containing protein | ||
| PP_RS15980 | 3473601..3474107 | - | 507 | WP_010953984.1 | sigma-70 family RNA polymerase sigma factor | ||
| PP_RS15985 | 3474196..3476712 | - | 2517 | WP_010953985.1 | excinuclease ABC subunit UvrA | ||
| T6CP009578 | TssA | PP_RS15990 (tssA) | 3476880..3477965 | - | 1086 | WP_010953986.1 | type VI secretion system protein TssA |
| T6CP009579 | TssD | PP_RS15995 | 3478061..3478579 | - | 519 | WP_049586088.1 | type VI secretion system tube protein Hcp |
| T6CP000096 | TssM | PP_RS16000 (tssM) | 3478723..3481218 | - | 2496 | WP_010953988.1 | type VI secretion system membrane subunit TssM |
| PP_RS16005 (tagF) | 3481215..3482123 | - | 909 | WP_049586086.1 | type VI secretion system-associated protein TagF | ||
| T6CP000097 | TssM | PP_RS16010 | 3482120..3485923 | - | 3804 | WP_010953989.1 | hypothetical protein |
| T6CP009581 | TssL | PP_RS16015 (icmH) | 3485954..3486670 | - | 717 | WP_010953990.1 | type IVB secretion system protein IcmH/DotU |
| T6CP000098 | TssK | PP_RS16020 (tssK) | 3486667..3488010 | - | 1344 | WP_010953991.1 | type VI secretion system baseplate subunit TssK |
| T6CP000099 | TssJ | PP_RS16025 (tssJ) | 3488007..3488729 | - | 723 | WP_004576638.1 | type VI secretion system lipoprotein TssJ |
| T6CP000100 | TssH | PP_RS16030 (tssH) | 3488754..3491351 | - | 2598 | WP_049586082.1 | type VI secretion system ATPase TssH |
| T6CP000101 | TssG | PP_RS16035 (tssG) | 3491348..3492418 | - | 1071 | WP_003248350.1 | type VI secretion system baseplate subunit TssG |
| T6CP000102 | TssF | PP_RS16040 (tssF) | 3492382..3494202 | - | 1821 | WP_010953993.1 | type VI secretion system baseplate subunit TssF |
| T6CP000103 | TssE | PP_RS16045 (tssE) | 3494202..3494684 | - | 483 | WP_003248355.1 | type VI secretion system baseplate subunit TssE |
| T6CP000104 | TssC | PP_RS16050 (tssC) | 3494711..3496213 | - | 1503 | WP_003248356.1 | type VI secretion system contractile sheath large subunit |
| T6CP000105 | TssB | PP_RS16055 (tssB) | 3496228..3496767 | - | 540 | WP_049586301.1 | type VI secretion system contractile sheath small subunit |
| PP_RS16060 | 3496832..3497581 | - | 750 | WP_049586080.1 | hypothetical protein | ||
| PP_RS16065 | 3498302..3498853 | - | 552 | WP_003248365.1 | hypothetical protein | ||
| PP_RS16070 | 3499064..3499783 | + | 720 | pseudogene | ADP-ribosylglycohydrolase family protein | ||
| PP_RS16075 | 3500053..3500325 | - | 273 | WP_061405645.1 | hypothetical protein | ||
| PP_RS28435 | 3500335..3500803 | - | 469 | pseudogene | hypothetical protein | ||
| PP_RS16085 | 3501267..3501455 | + | 189 | pseudogene | type VI secretion system tip protein VgrG | ||
| PP_RS16090 | 3501614..3502312 | + | 699 | WP_003248379.1 | hypothetical protein | ||
| PP_RS16095 | 3502346..3502605 | + | 260 | pseudogene | hypothetical protein | ||
| PP_RS28395 | 3502579..3502684 | - | 106 | pseudogene | hypothetical protein | ||
| PP_RS16105 | 3502704..3503015 | - | 312 | WP_049586073.1 | hypothetical protein | ||
| PP_RS16110 | 3503425..3503814 | - | 390 | WP_079732522.1 | reverse transcriptase | ||
| PP_RS16115 | 3503869..3504185 | - | 317 | pseudogene | hypothetical protein | ||
| PP_RS16120 | 3504275..3504571 | - | 297 | WP_010953996.1 | hypothetical 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) |
|---|---|---|---|---|---|---|---|---|
| REG0074 |
PP_4373 (FleQ) | protein | c-di-GMP regulatory pathway | Pseudomonas putida KT2440 | chromosome (NC_002947) | 4963882..4965357 (-) | 26991062 | K1-T6SS (hcp1) expression (↑) |
| REG0075 |
PP_0952 (RopN) | protein | c-di-GMP regulatory pathway | Pseudomonas putida KT2440 | chromosome (NC_002947) | 1094567..1096060 (-) | 26987688 | PP_4373 (FleQ) (↑) |
| REG0076 |
PP_0914 (BifA) | protein | c-di-GMP regulatory pathway | Pseudomonas putida KT2440 | chromosome (NC_002947) | 1055990..1058071 (-) | 26987650 | the levels of c-di-GMP (↓) |
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 |
|---|---|---|---|---|---|---|---|
| EFF01838 |
PP_3108 (Tke2) | Tde | IMU00355 |
Pseudomonas putida KT2440 | chromosome (NC_002947) | 3511333..3515490 (+) | 499256461 |
| EFF01837 |
PP_3089 (hcp1) | - | - | Pseudomonas putida KT2440 | chromosome (NC_002947) | 3478061..3478579 (-) | 898330886 |
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 |
|---|---|---|---|---|---|---|
| IMU00355 |
PP_5576 (Tki2) | EFF01838 |
Pseudomonas putida KT2440 | chromosome (NC_002947) | 3515484..3515960 (+) | 898330862 |
Experimental investigation has been performed.| Accessory protein ID | Locus tag (Gene) | Type | Organism | Replicon (Accession) | Coordinates (Strand) | NCBI ID | Related structure protein | Related effector |
|---|---|---|---|---|---|---|---|---|
| ACP00009 |
PP_RS16060 (tagB1) | structure affiliated protein | Pseudomonas putida KT2440 | chromosome (NC_002947) | 3496832..3497581 (-) | 898330878 | PP_RS15990 (TssA) | - |