Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 116005 |
| Name | oriT_pIsolateH_C  |
| Organism | Citrobacter freundii strain isolateH |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP135468 (45625..45730 [+], 106 nt) |
| oriT length | 106 nt |
| IRs (inverted repeats) | 30..35, 41..46 (CCGCCG..CGGCGG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 106 nt
>oriT_pIsolateH_C
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 10231 | GenBank | WP_004187323 |
| Name | traI_RRL14_RS25395_pIsolateH_C |
UniProt ID | A0A3U8KUL3 |
| Length | 659 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 659 a.a. Molecular weight: 75179.89 Da Isoelectric Point: 9.9948
>WP_004187323.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A3U8KUL3 |
T4CP
| ID | 11954 | GenBank | WP_004206885 |
| Name | t4cp2_RRL14_RS25075_pIsolateH_C |
UniProt ID | _ |
| Length | 695 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 695 a.a. Molecular weight: 79538.91 Da Isoelectric Point: 4.8317
>WP_004206885.1 MULTISPECIES: conjugal transfer protein TrbC [Enterobacterales]
MQQESVDSKKVLRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
MQQESVDSKKVLRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 48526..67815
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RRL14_RS25375 (RRL14_25375) | 43610..43921 | + | 312 | WP_004187333 | hypothetical protein | - |
| RRL14_RS25380 (RRL14_25380) | 44054..44590 | + | 537 | WP_004187332 | hypothetical protein | - |
| RRL14_RS25385 (RRL14_25385) | 45092..45487 | - | 396 | WP_019725163 | hypothetical protein | - |
| RRL14_RS25390 (RRL14_25390) | 45522..46049 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| RRL14_RS25395 (RRL14_25395) | 46036..48015 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| RRL14_RS25400 (RRL14_25400) | 48029..48529 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| RRL14_RS25405 (RRL14_25405) | 48526..49305 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| RRL14_RS25410 (RRL14_25410) | 49316..50479 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| RRL14_RS25415 (RRL14_25415) | 50469..50729 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| RRL14_RS25420 (RRL14_25420) | 50754..54191 | + | 3438 | WP_015586048 | LPD7 domain-containing protein | - |
| RRL14_RS25425 (RRL14_25425) | 54157..54669 | + | 513 | WP_011091071 | hypothetical protein | traL |
| RRL14_RS25430 (RRL14_25430) | 54670..54882 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| RRL14_RS25435 (RRL14_25435) | 54854..55264 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| RRL14_RS25440 (RRL14_25440) | 55332..56045 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| RRL14_RS25445 (RRL14_25445) | 56054..57205 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| RRL14_RS25450 (RRL14_25450) | 57217..58566 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| RRL14_RS25455 (RRL14_25455) | 58578..59282 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| RRL14_RS25460 (RRL14_25460) | 59306..59836 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| RRL14_RS25465 (RRL14_25465) | 59853..60242 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| RRL14_RS25470 (RRL14_25470) | 60288..60782 | + | 495 | WP_004187480 | hypothetical protein | - |
| RRL14_RS25475 (RRL14_25475) | 60779..63829 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| RRL14_RS25480 (RRL14_25480) | 63826..65034 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| RRL14_RS25485 (RRL14_25485) | 65031..65627 | + | 597 | WP_015060003 | hypothetical protein | - |
| RRL14_RS25490 (RRL14_25490) | 65620..67815 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| RRL14_RS25495 (RRL14_25495) | 67817..68470 | + | 654 | WP_015060005 | hypothetical protein | - |
| RRL14_RS25500 (RRL14_25500) | 68539..68781 | + | 243 | WP_023893611 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 16438 | GenBank | NZ_CP135468 |
| Plasmid name | pIsolateH_C | Incompatibility group | IncL/M |
| Plasmid size | 69064 bp | Coordinate of oriT [Strand] | 45625..45730 [+] |
| Host baterium | Citrobacter freundii strain isolateH |
Cargo genes
| Drug resistance gene | blaOXA-48 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |