Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121126 |
| Name | oriT_pF3221-3  |
| Organism | Citrobacter freundii strain F3221 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP137199 (7080..7161 [-], 82 nt) |
| oriT length | 82 nt |
| IRs (inverted repeats) | 27..32, 35..40 (GCCACC..GGTGGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 82 nt
>oriT_pF3221-3
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13336 | GenBank | WP_032440569 |
| Name | traI_R5Q27_RS00025_pF3221-3 |
UniProt ID | A0A7G3L4G1 |
| Length | 642 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 642 a.a. Molecular weight: 74384.24 Da Isoelectric Point: 8.3203
>WP_032440569.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDERFQRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVICQHNLMSVETAAMEMNSIAMQNTHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSPRSAEMVKQSVQTSYSDKLHVRDRGA
RAERRQARADARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASDNI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGSFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDDRYYD
DVRHNDDSSYKP
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDERFQRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVICQHNLMSVETAAMEMNSIAMQNTHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSPRSAEMVKQSVQTSYSDKLHVRDRGA
RAERRQARADARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASDNI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGSFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDDRYYD
DVRHNDDSSYKP
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A7G3L4G1 |
T4CP
| ID | 15625 | GenBank | WP_284237384 |
| Name | trbC_R5Q27_RS00300_pF3221-3 |
UniProt ID | _ |
| Length | 730 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 730 a.a. Molecular weight: 82678.80 Da Isoelectric Point: 6.4569
>WP_284237384.1 F-type conjugative transfer protein TrbC [Citrobacter freundii]
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPNTVQRATQLLSLAAAVLTETRGRYRVEYPEP
EKLSVKKNELEKYQHIHQSAVTQQADGFSY
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPNTVQRATQLLSLAAAVLTETRGRYRVEYPEP
EKLSVKKNELEKYQHIHQSAVTQQADGFSY
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 47193..69126
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| R5Q27_RS00285 (R5Q27_00285) | 42956..43582 | - | 627 | WP_254913868 | RepA family replication protein | - |
| R5Q27_RS00290 (R5Q27_00290) | 44157..44408 | - | 252 | WP_113394424 | hypothetical protein | - |
| R5Q27_RS00295 (R5Q27_00295) | 44420..44953 | - | 534 | WP_032440594 | phospholipase D family protein | - |
| R5Q27_RS00300 (R5Q27_00300) | 44999..47191 | - | 2193 | WP_284237384 | F-type conjugative transfer protein TrbC | - |
| R5Q27_RS00305 (R5Q27_00305) | 47193..48284 | - | 1092 | WP_050597336 | thioredoxin fold domain-containing protein | trbB |
| R5Q27_RS00310 (R5Q27_00310) | 48295..49713 | - | 1419 | WP_063666705 | hypothetical protein | trbA |
| R5Q27_RS00315 (R5Q27_00315) | 49815..50438 | - | 624 | WP_032440592 | plasmid IncI1-type surface exclusion protein ExcA | - |
| R5Q27_RS00320 (R5Q27_00320) | 50504..52648 | - | 2145 | WP_032440591 | DotA/TraY family protein | traY |
| R5Q27_RS00325 (R5Q27_00325) | 52690..53271 | - | 582 | WP_050597335 | conjugal transfer protein TraX | - |
| R5Q27_RS00330 (R5Q27_00330) | 53268..54464 | - | 1197 | WP_032440590 | conjugal transfer protein TraW | traW |
| R5Q27_RS00335 (R5Q27_00335) | 54474..57521 | - | 3048 | WP_032440589 | conjugal transfer protein | traU |
| R5Q27_RS00340 (R5Q27_00340) | 57531..58094 | - | 564 | WP_045325070 | hypothetical protein | traT |
| R5Q27_RS00345 (R5Q27_00345) | 58138..58539 | - | 402 | WP_032440588 | DUF6750 family protein | traR |
| R5Q27_RS00350 (R5Q27_00350) | 58595..59128 | - | 534 | WP_032440587 | conjugal transfer protein TraQ | traQ |
| R5Q27_RS00355 (R5Q27_00355) | 59138..59857 | - | 720 | WP_050597333 | conjugal transfer protein TraP | traP |
| R5Q27_RS00360 (R5Q27_00360) | 59864..61204 | - | 1341 | WP_032440586 | conjugal transfer protein TraO | traO |
| R5Q27_RS00365 (R5Q27_00365) | 61208..62311 | - | 1104 | WP_077264204 | DotH/IcmK family type IV secretion protein | traN |
| R5Q27_RS00370 (R5Q27_00370) | 62322..62990 | - | 669 | WP_032440585 | DotI/IcmL/TraM family protein | traM |
| R5Q27_RS00375 (R5Q27_00375) | 63062..63415 | - | 354 | WP_032440584 | hypothetical protein | traL |
| R5Q27_RS00380 (R5Q27_00380) | 63449..66862 | - | 3414 | WP_052145516 | LPD7 domain-containing protein | - |
| R5Q27_RS00385 (R5Q27_00385) | 66880..67146 | - | 267 | WP_032440577 | IcmT/TraK family protein | traK |
| R5Q27_RS00390 (R5Q27_00390) | 67143..68330 | - | 1188 | WP_077255878 | plasmid transfer ATPase TraJ | virB11 |
| R5Q27_RS00395 (R5Q27_00395) | 68308..69126 | - | 819 | WP_032440576 | type IV secretory system conjugative DNA transfer family protein | traI |
| R5Q27_RS00400 (R5Q27_00400) | 69123..69587 | - | 465 | WP_225546581 | DotD/TraH family lipoprotein | - |
| R5Q27_RS00405 (R5Q27_00405) | 69613..70092 | - | 480 | WP_032440574 | lytic transglycosylase domain-containing protein | - |
| R5Q27_RS00410 (R5Q27_00410) | 70105..70710 | - | 606 | WP_159376548 | hypothetical protein | - |
| R5Q27_RS00415 (R5Q27_00415) | 70824..71051 | - | 228 | WP_032440573 | hypothetical protein | - |
Host bacterium
| ID | 21554 | GenBank | NZ_CP137199 |
| Plasmid name | pF3221-3 | Incompatibility group | IncFII |
| Plasmid size | 71155 bp | Coordinate of oriT [Strand] | 7080..7161 [-] |
| Host baterium | Citrobacter freundii strain F3221 |
Cargo genes
| Drug resistance gene | tet(A), dfrA1, qacE, sul1, qnrS1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |