Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120611 |
| Name | oriT_18|P4  |
| Organism | Citrobacter freundii isolate 18 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OW849403 (39160..39265 [+], 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_18|P4
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12982 | GenBank | WP_004187323 |
| Name | traI_LQ111_RS26960_18|P4 |
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 | 15244 | GenBank | WP_004206885 |
| Name | t4cp2_LQ111_RS26670_18|P4 |
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: 42061..61350
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| LQ111_RS26940 (AI2680V1_5252) | 37145..37456 | + | 312 | WP_004187333 | hypothetical protein | - |
| LQ111_RS26945 (AI2680V1_5253) | 37589..38125 | + | 537 | WP_004187332 | hypothetical protein | - |
| LQ111_RS26950 (AI2680V1_5255) | 38627..39022 | - | 396 | WP_019725163 | hypothetical protein | - |
| LQ111_RS26955 | 39057..39584 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| LQ111_RS26960 (AI2680V1_5257) | 39571..41550 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| LQ111_RS26965 (AI2680V1_5258) | 41564..42064 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| LQ111_RS26970 (AI2680V1_5259) | 42061..42840 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| LQ111_RS26975 (AI2680V1_5260) | 42851..44014 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| LQ111_RS26980 (AI2680V1_5261) | 44004..44264 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| LQ111_RS26985 (AI2680V1_5262) | 44289..47726 | + | 3438 | WP_015586048 | LPD7 domain-containing protein | - |
| LQ111_RS26990 (AI2680V1_5263) | 47692..48204 | + | 513 | WP_011091071 | hypothetical protein | traL |
| LQ111_RS26995 (AI2680V1_5264) | 48205..48417 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| LQ111_RS27000 (AI2680V1_5265) | 48389..48799 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| LQ111_RS27005 (AI2680V1_5266) | 48867..49580 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| LQ111_RS27010 (AI2680V1_5267) | 49589..50740 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| LQ111_RS27015 (AI2680V1_5268) | 50752..52101 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| LQ111_RS27020 (AI2680V1_5269) | 52113..52817 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| LQ111_RS27025 (AI2680V1_5270) | 52841..53371 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| LQ111_RS27030 (AI2680V1_5271) | 53388..53777 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| LQ111_RS27035 (AI2680V1_5272) | 53823..54317 | + | 495 | WP_004187480 | hypothetical protein | - |
| LQ111_RS27040 (AI2680V1_5273) | 54314..57364 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| LQ111_RS27045 (AI2680V1_5274) | 57361..58569 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| LQ111_RS27050 (AI2680V1_5275) | 58566..59162 | + | 597 | WP_015060003 | hypothetical protein | - |
| LQ111_RS27055 (AI2680V1_5276) | 59155..61350 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| LQ111_RS27060 (AI2680V1_5277) | 61352..62005 | + | 654 | WP_015060005 | hypothetical protein | - |
| LQ111_RS27065 (AI2680V1_5278) | 62086..62316 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 21040 | GenBank | NZ_OW849403 |
| Plasmid name | 18|P4 | Incompatibility group | IncL/M |
| Plasmid size | 62611 bp | Coordinate of oriT [Strand] | 39160..39265 [+] |
| Host baterium | Citrobacter freundii isolate 18 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |