Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 108142 |
| Name | oriT_CF13|pOXA-48  |
| Organism | Citrobacter freundii strain CF13 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP124810 (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_CF13|pOXA-48
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 5457 | GenBank | WP_004187323 |
| Name | Relaxase_QLG16_RS24860_CF13|pOXA-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 | 5804 | GenBank | WP_004206885 |
| Name | t4cp2_QLG16_RS24565_CF13|pOXA-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 |
|---|---|---|---|---|---|---|
| QLG16_RS24840 (QLG16_24840) | 38123..38434 | + | 312 | WP_004187333 | hypothetical protein | - |
| QLG16_RS24845 (QLG16_24845) | 38567..39103 | + | 537 | WP_193796351 | hypothetical protein | - |
| QLG16_RS24850 (QLG16_24850) | 39605..40000 | - | 396 | WP_019725163 | hypothetical protein | - |
| QLG16_RS24855 (QLG16_24855) | 40035..40562 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| QLG16_RS24860 (QLG16_24860) | 40549..42528 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| QLG16_RS24865 (QLG16_24865) | 42542..43042 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| QLG16_RS24870 (QLG16_24870) | 43039..43818 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| QLG16_RS24875 (QLG16_24875) | 43829..44992 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| QLG16_RS24880 (QLG16_24880) | 44982..45242 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| QLG16_RS24885 (QLG16_24885) | 45267..48704 | + | 3438 | WP_015586048 | LPD7 domain-containing protein | - |
| QLG16_RS24890 (QLG16_24890) | 48670..49182 | + | 513 | WP_011091071 | hypothetical protein | traL |
| QLG16_RS24895 (QLG16_24895) | 49183..49395 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| QLG16_RS24900 (QLG16_24900) | 49367..49777 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| QLG16_RS24905 (QLG16_24905) | 49845..50558 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| QLG16_RS24910 (QLG16_24910) | 50567..51718 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| QLG16_RS24915 (QLG16_24915) | 51730..53079 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| QLG16_RS24920 (QLG16_24920) | 53091..53795 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| QLG16_RS24925 (QLG16_24925) | 53819..54349 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| QLG16_RS24930 (QLG16_24930) | 54366..54755 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| QLG16_RS24935 (QLG16_24935) | 54801..55295 | + | 495 | WP_004187480 | hypothetical protein | - |
| QLG16_RS24940 (QLG16_24940) | 55292..58342 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| QLG16_RS24945 (QLG16_24945) | 58339..59547 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| QLG16_RS24950 (QLG16_24950) | 59544..60140 | + | 597 | WP_015060003 | hypothetical protein | - |
| QLG16_RS24955 (QLG16_24955) | 60133..62328 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| QLG16_RS24960 (QLG16_24960) | 62330..62983 | + | 654 | WP_015060005 | hypothetical protein | - |
| QLG16_RS24965 (QLG16_24965) | 63064..63294 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 8577 | GenBank | NZ_CP124810 |
| Plasmid name | CF13|pOXA-48 | Incompatibility group | IncL/M |
| Plasmid size | 63589 bp | Coordinate of oriT [Strand] | 40138..40243 [+] |
| Host baterium | Citrobacter freundii strain CF13 |
Cargo genes
| Drug resistance gene | blaOXA-48 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |