Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106078 |
| Name | oriT_pACV-OXA-48  |
| Organism | Citrobacter freundii strain zone4 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP045727 (40138..40243 [+], 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_pACV-OXA-48
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4079 | GenBank | WP_004187323 |
| Name | Relaxase_GHT30_RS23690_pACV-OXA-48 |
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 | 4092 | GenBank | WP_004206885 |
| Name | t4cp2_GHT30_RS23395_pACV-OXA-48 |
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: 43039..62328
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| GHT30_RS23670 (GHT30_23665) | 38123..38434 | + | 312 | WP_004187333 | hypothetical protein | - |
| GHT30_RS23675 (GHT30_23670) | 38567..39103 | + | 537 | WP_004187332 | hypothetical protein | - |
| GHT30_RS23680 (GHT30_23675) | 39605..40000 | - | 396 | WP_019725163 | hypothetical protein | - |
| GHT30_RS23960 | 40035..40562 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| GHT30_RS23690 (GHT30_23685) | 40549..42528 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| GHT30_RS23695 (GHT30_23690) | 42542..43042 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| GHT30_RS23700 (GHT30_23695) | 43039..43818 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| GHT30_RS23705 (GHT30_23700) | 43829..44992 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| GHT30_RS23710 (GHT30_23705) | 44982..45242 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| GHT30_RS23965 | 45267..48704 | + | 3438 | WP_015586048 | LPD7 domain-containing protein | - |
| GHT30_RS23720 (GHT30_23715) | 48670..49182 | + | 513 | WP_011091071 | hypothetical protein | traL |
| GHT30_RS23725 (GHT30_23720) | 49183..49395 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| GHT30_RS23730 (GHT30_23725) | 49367..49777 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| GHT30_RS23735 (GHT30_23730) | 49845..50558 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| GHT30_RS23740 (GHT30_23735) | 50567..51718 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| GHT30_RS23745 (GHT30_23740) | 51730..53079 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| GHT30_RS23750 (GHT30_23745) | 53091..53795 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| GHT30_RS23755 (GHT30_23750) | 53819..54349 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| GHT30_RS23760 (GHT30_23755) | 54366..54755 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| GHT30_RS23765 (GHT30_23760) | 54801..55295 | + | 495 | WP_004187480 | hypothetical protein | - |
| GHT30_RS23770 (GHT30_23765) | 55292..58342 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| GHT30_RS23775 (GHT30_23770) | 58339..59547 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| GHT30_RS23780 (GHT30_23775) | 59544..60140 | + | 597 | WP_015060003 | hypothetical protein | - |
| GHT30_RS23785 (GHT30_23780) | 60133..62328 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| GHT30_RS23790 (GHT30_23785) | 62330..62983 | + | 654 | WP_015060005 | hypothetical protein | - |
| GHT30_RS23795 (GHT30_23790) | 63064..63294 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 6515 | GenBank | NZ_CP045727 |
| Plasmid name | pACV-OXA-48 | Incompatibility group | IncL/M |
| Plasmid size | 63589 bp | Coordinate of oriT [Strand] | 40138..40243 [+] |
| Host baterium | Citrobacter freundii strain zone4 |
Cargo genes
| Drug resistance gene | blaOXA-48 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |