Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 111839 |
| Name | oriT_C. freundii 18|P4  |
| Organism | Citrobacter freundii isolate 18 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OW849212 (40119..40224 [+], 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_C. freundii 18|P4
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 7677 | GenBank | WP_004187323 |
| Name | traI_LQ122_RS27230_C. freundii 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 | 8771 | GenBank | WP_004206885 |
| Name | t4cp2_LQ122_RS26935_C. freundii 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: 43020..62309
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| LQ122_RS27210 (AI2668V1_5307) | 38104..38415 | + | 312 | WP_004187333 | hypothetical protein | - |
| LQ122_RS27215 (AI2668V1_5308) | 38548..39084 | + | 537 | WP_004187332 | hypothetical protein | - |
| LQ122_RS27220 (AI2668V1_5310) | 39586..39981 | - | 396 | WP_019725163 | hypothetical protein | - |
| LQ122_RS27225 | 40016..40543 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| LQ122_RS27230 (AI2668V1_5312) | 40530..42509 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| LQ122_RS27235 (AI2668V1_5313) | 42523..43023 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| LQ122_RS27240 (AI2668V1_5314) | 43020..43799 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| LQ122_RS27245 (AI2668V1_5315) | 43810..44973 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| LQ122_RS27250 (AI2668V1_5316) | 44963..45223 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| LQ122_RS27255 (AI2668V1_5317) | 45248..48685 | + | 3438 | WP_015586048 | LPD7 domain-containing protein | - |
| LQ122_RS27260 (AI2668V1_5318) | 48651..49163 | + | 513 | WP_011091071 | hypothetical protein | traL |
| LQ122_RS27265 (AI2668V1_5319) | 49164..49376 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| LQ122_RS27270 (AI2668V1_5320) | 49348..49758 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| LQ122_RS27275 (AI2668V1_5321) | 49826..50539 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| LQ122_RS27280 (AI2668V1_5322) | 50548..51699 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| LQ122_RS27285 (AI2668V1_5323) | 51711..53060 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| LQ122_RS27290 (AI2668V1_5324) | 53072..53776 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| LQ122_RS27295 (AI2668V1_5325) | 53800..54330 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| LQ122_RS27300 (AI2668V1_5326) | 54347..54736 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| LQ122_RS27305 (AI2668V1_5327) | 54782..55276 | + | 495 | WP_004187480 | hypothetical protein | - |
| LQ122_RS27310 (AI2668V1_5328) | 55273..58323 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| LQ122_RS27315 (AI2668V1_5329) | 58320..59528 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| LQ122_RS27320 (AI2668V1_5330) | 59525..60121 | + | 597 | WP_015060003 | hypothetical protein | - |
| LQ122_RS27325 (AI2668V1_5331) | 60114..62309 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| LQ122_RS27330 (AI2668V1_5332) | 62311..62964 | + | 654 | WP_015060005 | hypothetical protein | - |
| LQ122_RS27335 (AI2668V1_5333) | 63045..63275 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 12274 | GenBank | NZ_OW849212 |
| Plasmid name | C. freundii 18|P4 | Incompatibility group | IncL/M |
| Plasmid size | 63570 bp | Coordinate of oriT [Strand] | 40119..40224 [+] |
| Host baterium | Citrobacter freundii isolate 18 |
Cargo genes
| Drug resistance gene | blaOXA-48 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |