Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 111838 |
| Name | oriT_C. freundii 112|P4  |
| Organism | Citrobacter freundii isolate 112 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OW995945 (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_C. freundii 112|P4
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 7676 | GenBank | WP_004187323 |
| Name | traI_LQ198_RS27975_C. freundii 112|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 | 8770 | GenBank | WP_004206885 |
| Name | t4cp2_LQ198_RS27680_C. freundii 112|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: 43039..62328
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| LQ198_RS27955 (AI2935V1_5495) | 38123..38434 | + | 312 | WP_004187333 | hypothetical protein | - |
| LQ198_RS27960 (AI2935V1_5496) | 38567..39103 | + | 537 | WP_004187332 | hypothetical protein | - |
| LQ198_RS27965 (AI2935V1_5498) | 39605..40000 | - | 396 | WP_019725163 | hypothetical protein | - |
| LQ198_RS27970 | 40035..40562 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| LQ198_RS27975 (AI2935V1_5500) | 40549..42528 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| LQ198_RS27980 (AI2935V1_5501) | 42542..43042 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| LQ198_RS27985 (AI2935V1_5502) | 43039..43818 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| LQ198_RS27990 (AI2935V1_5503) | 43829..44992 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| LQ198_RS27995 (AI2935V1_5504) | 44982..45242 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| LQ198_RS28000 (AI2935V1_5505) | 45267..48704 | + | 3438 | WP_015586048 | LPD7 domain-containing protein | - |
| LQ198_RS28005 (AI2935V1_5506) | 48670..49182 | + | 513 | WP_011091071 | hypothetical protein | traL |
| LQ198_RS28010 (AI2935V1_5507) | 49183..49395 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| LQ198_RS28015 (AI2935V1_5508) | 49367..49777 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| LQ198_RS28020 (AI2935V1_5509) | 49845..50558 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| LQ198_RS28025 (AI2935V1_5510) | 50567..51718 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| LQ198_RS28030 (AI2935V1_5511) | 51730..53079 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| LQ198_RS28035 (AI2935V1_5512) | 53091..53795 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| LQ198_RS28040 (AI2935V1_5513) | 53819..54349 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| LQ198_RS28045 (AI2935V1_5514) | 54366..54755 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| LQ198_RS28050 (AI2935V1_5515) | 54801..55295 | + | 495 | WP_004187480 | hypothetical protein | - |
| LQ198_RS28055 (AI2935V1_5516) | 55292..58342 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| LQ198_RS28060 (AI2935V1_5517) | 58339..59547 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| LQ198_RS28065 (AI2935V1_5518) | 59544..60140 | + | 597 | WP_015060003 | hypothetical protein | - |
| LQ198_RS28070 (AI2935V1_5519) | 60133..62328 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| LQ198_RS28075 (AI2935V1_5520) | 62330..62983 | + | 654 | WP_015060005 | hypothetical protein | - |
| LQ198_RS28080 (AI2935V1_5521) | 63064..63294 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 12273 | GenBank | NZ_OW995945 |
| Plasmid name | C. freundii 112|P4 | Incompatibility group | IncL/M |
| Plasmid size | 63589 bp | Coordinate of oriT [Strand] | 40138..40243 [+] |
| Host baterium | Citrobacter freundii isolate 112 |
Cargo genes
| Drug resistance gene | blaOXA-48 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |