Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114575 |
| Name | oriT_pKPC-2fe2  |
| Organism | Citrobacter sp. CFNIH10 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP026210 (961..1066 [-], 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_pKPC-2fe2
AGTACGGAACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGAACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9340 | GenBank | WP_004187323 |
| Name | traI_C2U53_RS00005_pKPC-2fe2 |
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 | 10835 | GenBank | WP_004187443 |
| Name | t4cp2_C2U53_RS00265_pKPC-2fe2 |
UniProt ID | _ |
| Length | 695 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 695 a.a. Molecular weight: 79519.87 Da Isoelectric Point: 4.8309
>WP_004187443.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMHFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMHFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 56437..75750
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| C2U53_RS30600 | 52800..52895 | - | 96 | WP_004206884 | DinQ-like type I toxin DqlB | - |
| C2U53_RS00385 (C2U53_00385) | 54118..55173 | - | 1056 | WP_015060006 | plasmid replication initiator RepA | - |
| C2U53_RS00390 (C2U53_00390) | 55470..55718 | - | 249 | WP_015062836 | IncL/M type plasmid replication protein RepC | - |
| C2U53_RS00395 (C2U53_00395) | 55782..56435 | - | 654 | WP_040119745 | hypothetical protein | - |
| C2U53_RS00400 (C2U53_00400) | 56437..58632 | - | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| C2U53_RS00405 (C2U53_00405) | 58625..59221 | - | 597 | WP_015060003 | hypothetical protein | - |
| C2U53_RS00410 (C2U53_00410) | 59218..60426 | - | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| C2U53_RS00415 (C2U53_00415) | 60423..63473 | - | 3051 | WP_040119746 | conjugal transfer protein | traU |
| C2U53_RS00420 (C2U53_00420) | 63470..63964 | - | 495 | WP_011091080 | hypothetical protein | - |
| C2U53_RS00425 (C2U53_00425) | 64010..64399 | - | 390 | WP_011091078 | DUF6750 family protein | traR |
| C2U53_RS00430 (C2U53_00430) | 64416..64946 | - | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| C2U53_RS00435 (C2U53_00435) | 64970..65674 | - | 705 | WP_040119747 | conjugal transfer protein TraP | traP |
| C2U53_RS00440 (C2U53_00440) | 65686..67035 | - | 1350 | WP_040119748 | conjugal transfer protein TraO | traO |
| C2U53_RS00445 (C2U53_00445) | 67047..68177 | - | 1131 | WP_077255002 | DotH/IcmK family type IV secretion protein | traN |
| C2U53_RS00450 (C2U53_00450) | 68186..68899 | - | 714 | WP_223430951 | DotI/IcmL family type IV secretion protein | traM |
| C2U53_RS00455 (C2U53_00455) | 68967..69377 | + | 411 | WP_040027863 | H-NS family nucleoid-associated regulatory protein | - |
| C2U53_RS00460 (C2U53_00460) | 69427..69561 | + | 135 | WP_229654975 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| C2U53_RS00465 (C2U53_00465) | 69562..70074 | - | 513 | WP_011091071 | hypothetical protein | traL |
| C2U53_RS30160 | 70040..73522 | - | 3483 | WP_227022524 | LPD7 domain-containing protein | - |
| C2U53_RS00480 (C2U53_00480) | 73547..73807 | - | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| C2U53_RS00485 (C2U53_00485) | 73797..74960 | - | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| C2U53_RS00490 (C2U53_00490) | 74971..75750 | - | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| C2U53_RS00495 (C2U53_00495) | 75747..76247 | - | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
Host bacterium
| ID | 15010 | GenBank | NZ_CP026210 |
| Plasmid name | pKPC-2fe2 | Incompatibility group | IncL/M |
| Plasmid size | 77585 bp | Coordinate of oriT [Strand] | 961..1066 [-] |
| Host baterium | Citrobacter sp. CFNIH10 |
Cargo genes
| Drug resistance gene | ant(2'')-Ia, blaTEM-1A, blaOXA-9, ant(3'')-Ia, aac(6')-Ib, blaKPC-2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |