Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100146 |
| Name | oriT_pTer331  |
| Organism | Collimonas fungivorans Ter331 |
| Sequence Completeness | incomplete |
| NCBI accession of oriT (coordinates [strand]) | NC_010332 (10770..10811 [-], 42 nt) |
| oriT length | 42 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | 24..25 |
| Conserved sequence flanking the nic site |
TATCCTG|C |
| Note | The putative oriT site with 100% identity to that described for pIPO2 (Tauch et al., 2002). |
oriT sequence
Download Length: 42 nt
>oriT_pTer331
TATACCGGCGATTAGCCTATCCTGCAATAGCCCACACCCCCC
TATACCGGCGATTAGCCTATCCTGCAATAGCCCACACCCCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Mela F et al. (2008) Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol. 66(1):45-62. [PMID:18355297]
Relaxase
| ID | 140 | GenBank | YP_001672039 |
| Name | TraR/VirD2_pTer331 |
UniProt ID | B0ZB68 |
| Length | 364 a.a. | PDB ID | |
| Note | nickase/relaxase activity | ||
Relaxase protein sequence
Download Length: 364 a.a. Molecular weight: 40370.63 Da Isoelectric Point: 10.5774
>YP_001672039.1 hypothetical protein pTer331_13 (plasmid) [Collimonas fungivorans Ter331]
MSKTVIDGIIKDWGERLHYSPVKGSKGRNIRSGGTTRAAKPAPPSGPATKEKVARTAKKTAEVMVKISGG
GKNMKHIKAHMDYISRNGEVEIEDENGDIHQGMEAVRDVRDSWAKGKIGIPYEGEKRKEAFNIVLSMPPG
TDRQAVKDAAREFAKQEFGNHQYVFAAHDDEKHPHVHLAVKAVGNDGIRLNPRKGDLQFWREQFAEKLRD
QGIEANATPRRARGVVQKAEKQAVRHIDAEFERGKRQEPARVTRARKRDAEAEVTTGKKRANPAQDNISA
ARKDTQKAYGQIARALATGEAEDKQIALNIVRLVQTMPPVVTKHEALVQSLHGTGGKLAGREAEPKQPKR
QEQGRAKPDDEQTR
MSKTVIDGIIKDWGERLHYSPVKGSKGRNIRSGGTTRAAKPAPPSGPATKEKVARTAKKTAEVMVKISGG
GKNMKHIKAHMDYISRNGEVEIEDENGDIHQGMEAVRDVRDSWAKGKIGIPYEGEKRKEAFNIVLSMPPG
TDRQAVKDAAREFAKQEFGNHQYVFAAHDDEKHPHVHLAVKAVGNDGIRLNPRKGDLQFWREQFAEKLRD
QGIEANATPRRARGVVQKAEKQAVRHIDAEFERGKRQEPARVTRARKRDAEAEVTTGKKRANPAQDNISA
ARKDTQKAYGQIARALATGEAEDKQIALNIVRLVQTMPPVVTKHEALVQSLHGTGGKLAGREAEPKQPKR
QEQGRAKPDDEQTR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B0ZB68 |
Reference
[1] Mela F et al. (2008) Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol. 66(1):45-62. [PMID:18355297]
T4CP
| ID | 140 | GenBank | YP_001672044 |
| Name | TraN/VirD4_pTer331 |
UniProt ID | B0ZB73 |
| Length | 900 a.a. | PDB ID | _ |
| Note | ATPase, coupling the relaxosome with the transfer machinery | ||
T4CP protein sequence
Download Length: 900 a.a. Molecular weight: 98307.53 Da Isoelectric Point: 4.3744
>YP_001672044.1 hypothetical protein pTer331_18 (plasmid) [Collimonas fungivorans Ter331]
MEMPKWLKWVLGVVVFIAATVGAVWLAGFFFFAFSKTNPFGKTDFSTWWTYWQFYQADPVIAKRLKVSGI
VAAVVAYGAPIVALIAAMREVRSLHGEARFANASEIEKAGLFGNTGIIIGKLKNRFLMFAGMQFVLLAAP
TRSGKGVGVVIPNLLNWSESVVVLDVKLENFLITSKFRAKWGQEVYLFNPFSISEDAEGNPLNGRTHRYN
PLGYIGDDARLRVTDILAIGYSLYPGEGRDAFFDDAARNLFLGLTLYLCETPSLPRTMGELLRQSSGKGK
PVKQHIQGIVTERNFREFGDVMLNDVGEDQAEVVKAIMAAAGISEAEAEKLCDDAPIVVVKDVAAAEIEQ
VEALFKEAGAEVEVTRKLVPITQWDGVGLPPLTMECVDALNRFTATSDNTLSSIMASFNVPLTIWASPIV
DAATSANDFDLRDVRKKRMSIYLGIPANKLAEAKLLMNMFYTQLVNLNTNRLLHSSPELKYTVLMLDDEF
TAPGRIGIIDKANSYMAGYGLRMLNIIQSPGQLEAEAPKGYGRENARTFVTNHACQIFFTPREQRDANEY
SEALGYYTFKAKGSSRQLGGKAAGGRSESESDQKRALMMPQELKEMSQREQIISLENTKAIRCEKISYFS
DHVFVDRLKSVTPSLAKLGKKLPTKKQLEDAWGSGECAVSIPLLNLDLHEAVVQARSRALTVTDVAKGID
LRALALDFSKVPLPTGDGIEAEQVEAFVDGFFDALDAANEYDEDEAPDVDEDGASERPSDDELAALDAEA
ADDGGKVAVNTIEQADDEPAAAELVTGASRPGGGSVAKPEPQAEPEPEPDRGLGHDQADIEPDGPTDEDL
AAMMEDFTPPDDGMMDEADMLAALDEMEAVPEYVEEAENDAPILDLSVLDKPLPSIKNAK
MEMPKWLKWVLGVVVFIAATVGAVWLAGFFFFAFSKTNPFGKTDFSTWWTYWQFYQADPVIAKRLKVSGI
VAAVVAYGAPIVALIAAMREVRSLHGEARFANASEIEKAGLFGNTGIIIGKLKNRFLMFAGMQFVLLAAP
TRSGKGVGVVIPNLLNWSESVVVLDVKLENFLITSKFRAKWGQEVYLFNPFSISEDAEGNPLNGRTHRYN
PLGYIGDDARLRVTDILAIGYSLYPGEGRDAFFDDAARNLFLGLTLYLCETPSLPRTMGELLRQSSGKGK
PVKQHIQGIVTERNFREFGDVMLNDVGEDQAEVVKAIMAAAGISEAEAEKLCDDAPIVVVKDVAAAEIEQ
VEALFKEAGAEVEVTRKLVPITQWDGVGLPPLTMECVDALNRFTATSDNTLSSIMASFNVPLTIWASPIV
DAATSANDFDLRDVRKKRMSIYLGIPANKLAEAKLLMNMFYTQLVNLNTNRLLHSSPELKYTVLMLDDEF
TAPGRIGIIDKANSYMAGYGLRMLNIIQSPGQLEAEAPKGYGRENARTFVTNHACQIFFTPREQRDANEY
SEALGYYTFKAKGSSRQLGGKAAGGRSESESDQKRALMMPQELKEMSQREQIISLENTKAIRCEKISYFS
DHVFVDRLKSVTPSLAKLGKKLPTKKQLEDAWGSGECAVSIPLLNLDLHEAVVQARSRALTVTDVAKGID
LRALALDFSKVPLPTGDGIEAEQVEAFVDGFFDALDAANEYDEDEAPDVDEDGASERPSDDELAALDAEA
ADDGGKVAVNTIEQADDEPAAAELVTGASRPGGGSVAKPEPQAEPEPEPDRGLGHDQADIEPDGPTDEDL
AAMMEDFTPPDDGMMDEADMLAALDEMEAVPEYVEEAENDAPILDLSVLDKPLPSIKNAK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B0ZB73 |
Reference
[1] Mela F et al. (2008) Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol. 66(1):45-62. [PMID:18355297]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 20480..33184
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| G7B74_RS00090 (pTer331_17) | 16431..17129 | - | 699 | WP_012274942 | hypothetical protein | - |
| G7B74_RS00095 (pTer331_18) | 17230..19932 | - | 2703 | WP_012274943 | ribosomal protein L7/L12 | - |
| G7B74_RS00100 (pTer331_19) | 20480..21547 | - | 1068 | WP_168547971 | P-type DNA transfer ATPase VirB11 | virB11 |
| G7B74_RS00105 (pTer331_20) | 21531..22691 | - | 1161 | WP_012274945 | type IV secretion system protein VirB10 | virB10 |
| G7B74_RS00110 (pTer331_21) | 22691..23563 | - | 873 | WP_012274946 | P-type conjugative transfer protein VirB9 | virB9 |
| G7B74_RS00115 (pTer331_22) | 23560..24270 | - | 711 | WP_012274947 | VirB8/TrbF family protein | virB8 |
| G7B74_RS00120 (pTer331_23) | 24276..24440 | - | 165 | WP_012274948 | hypothetical protein | - |
| G7B74_RS00125 (pTer331_24) | 24577..25659 | - | 1083 | WP_012274949 | type IV secretion system protein | virB6 |
| G7B74_RS00130 (pTer331_25) | 25671..25967 | - | 297 | WP_012274950 | EexN family lipoprotein | - |
| G7B74_RS00135 (pTer331_26) | 26071..26784 | - | 714 | WP_168547975 | P-type DNA transfer protein VirB5 | virB5 |
| G7B74_RS00140 (pTer331_27) | 26796..29276 | - | 2481 | WP_012274952 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| G7B74_RS00145 (pTer331_28) | 29283..29594 | - | 312 | WP_238824245 | VirB3 family type IV secretion system protein | virB3 |
| G7B74_RS00150 (pTer331_29) | 29616..30044 | - | 429 | WP_238824247 | TrbC/VirB2 family protein | virB2 |
| G7B74_RS00155 (pTer331_30) | 30089..32404 | - | 2316 | WP_012274955 | type I DNA topoisomerase | - |
| G7B74_RS00160 (pTer331_31) | 32414..33184 | - | 771 | WP_012274956 | lytic transglycosylase domain-containing protein | virB1 |
| G7B74_RS00165 (pTer331_32) | 33242..33649 | - | 408 | WP_179894029 | hypothetical protein | - |
| G7B74_RS00170 (pTer331_33) | 34789..35097 | + | 309 | WP_012274958 | hypothetical protein | - |
| G7B74_RS00175 (pTer331_34) | 35119..35667 | + | 549 | WP_012274959 | hypothetical protein | - |
| G7B74_RS00180 (pTer331_35) | 35776..36042 | + | 267 | WP_012274960 | hypothetical protein | - |
| G7B74_RS00185 (pTer331_36) | 36130..36270 | + | 141 | WP_012274961 | hypothetical protein | - |
| G7B74_RS00190 (pTer331_37) | 36294..36563 | + | 270 | WP_238824248 | hypothetical protein | - |
| G7B74_RS00195 (pTer331_38) | 36574..37002 | + | 429 | WP_012274963 | hypothetical protein | - |
| G7B74_RS00200 (pTer331_39) | 36999..37136 | + | 138 | WP_012274964 | hypothetical protein | - |
| G7B74_RS00205 (pTer331_40) | 37157..37423 | + | 267 | WP_012274965 | hypothetical protein | - |
| G7B74_RS00210 (pTer331_41) | 37432..37695 | + | 264 | WP_154048552 | hypothetical protein | - |
Host bacterium
| ID | 140 | GenBank | NC_010332 |
| Plasmid name | pTer331 | Incompatibility group | PromA |
| Plasmid size | 40457 bp | Coordinate of oriT [Strand] | 10770..10811 [-] |
| Host baterium | Collimonas fungivorans Ter331 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |