Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 115794 |
| Name | oriT_64A:C|unnamed3  |
| Organism | Citrobacter portucalensis strain 64A:C |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP134687 (21281..21386 [-], 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_64A:C|unnamed3
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 10116 | GenBank | WP_004187323 |
| Name | traI_RIK60_RS25305_64A:C|unnamed3 |
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 | 11821 | GenBank | WP_004206885 |
| Name | t4cp2_RIK60_RS25605_64A:C|unnamed3 |
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: 1977..18485
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RIK60_RS25215 (RIK60_25215) | 1384..1980 | - | 597 | WP_015060003 | hypothetical protein | - |
| RIK60_RS25220 (RIK60_25220) | 1977..3185 | - | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| RIK60_RS25225 (RIK60_25225) | 3182..6232 | - | 3051 | WP_004187482 | hypothetical protein | traU |
| RIK60_RS25230 (RIK60_25230) | 6229..6723 | - | 495 | WP_004187480 | hypothetical protein | - |
| RIK60_RS25235 (RIK60_25235) | 6769..7158 | - | 390 | WP_004187479 | DUF6750 family protein | traR |
| RIK60_RS25240 (RIK60_25240) | 7175..7705 | - | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| RIK60_RS25245 (RIK60_25245) | 7729..8433 | - | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| RIK60_RS25250 (RIK60_25250) | 8445..9794 | - | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| RIK60_RS25255 (RIK60_25255) | 9806..10957 | - | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| RIK60_RS25260 (RIK60_25260) | 10966..11679 | - | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| RIK60_RS25265 (RIK60_25265) | 11747..12157 | + | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| RIK60_RS25270 (RIK60_25270) | 12186..12341 | + | 156 | WP_172693602 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| RIK60_RS25275 (RIK60_25275) | 12342..12854 | - | 513 | WP_011091071 | hypothetical protein | traL |
| RIK60_RS25280 (RIK60_25280) | 12820..16257 | - | 3438 | WP_015586048 | LPD7 domain-containing protein | - |
| RIK60_RS25285 (RIK60_25285) | 16282..16542 | - | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| RIK60_RS25290 (RIK60_25290) | 16532..17695 | - | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| RIK60_RS25295 (RIK60_25295) | 17706..18485 | - | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| RIK60_RS25300 (RIK60_25300) | 18482..18982 | - | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| RIK60_RS25305 (RIK60_25305) | 18996..20975 | - | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| RIK60_RS25310 (RIK60_25310) | 20962..21489 | - | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| RIK60_RS25315 (RIK60_25315) | 21524..21919 | + | 396 | WP_019725163 | hypothetical protein | - |
| RIK60_RS25320 (RIK60_25320) | 22421..22957 | - | 537 | WP_004187332 | hypothetical protein | - |
| RIK60_RS25325 (RIK60_25325) | 23090..23401 | - | 312 | WP_004187333 | hypothetical protein | - |
Host bacterium
| ID | 16227 | GenBank | NZ_CP134687 |
| Plasmid name | 64A:C|unnamed3 | Incompatibility group | IncL/M |
| Plasmid size | 64903 bp | Coordinate of oriT [Strand] | 21281..21386 [-] |
| Host baterium | Citrobacter portucalensis strain 64A:C |
Cargo genes
| Drug resistance gene | blaOXA-48 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |