Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114443 |
| Name | oriT_pKPC-56ce  |
| Organism | Serratia sp. SSNIH1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP026385 (24252..24357 [+], 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-56ce
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9259 | GenBank | WP_004187323 |
| Name | traI_C3F38_RS25790_pKPC-56ce |
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 | 10734 | GenBank | WP_004187443 |
| Name | t4cp2_C3F38_RS26040_pKPC-56ce |
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: 27153..46466
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| C3F38_RS25770 (C3F38_25765) | 22238..22549 | + | 312 | WP_011154461 | hypothetical protein | - |
| C3F38_RS25775 (C3F38_25770) | 22682..23218 | + | 537 | WP_040119830 | hypothetical protein | - |
| C3F38_RS25780 (C3F38_25775) | 23719..24114 | - | 396 | WP_170934351 | MobC | - |
| C3F38_RS26715 | 24149..24676 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| C3F38_RS25790 (C3F38_25785) | 24663..26642 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| C3F38_RS25795 (C3F38_25790) | 26656..27156 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| C3F38_RS25800 (C3F38_25795) | 27153..27932 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| C3F38_RS25805 (C3F38_25800) | 27943..29106 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| C3F38_RS25810 (C3F38_25805) | 29096..29356 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| C3F38_RS26720 | 29381..32863 | + | 3483 | WP_227022524 | LPD7 domain-containing protein | - |
| C3F38_RS26330 | 32829..33341 | + | 513 | WP_011091071 | hypothetical protein | traL |
| C3F38_RS25825 (C3F38_25820) | 33342..33476 | - | 135 | WP_229654975 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| C3F38_RS25830 (C3F38_25825) | 33526..33936 | - | 411 | WP_040027863 | H-NS family nucleoid-associated regulatory protein | - |
| C3F38_RS25835 (C3F38_25830) | 34004..34717 | + | 714 | WP_223430951 | DotI/IcmL family type IV secretion protein | traM |
| C3F38_RS25840 (C3F38_25835) | 34726..35856 | + | 1131 | WP_077255002 | DotH/IcmK family type IV secretion protein | traN |
| C3F38_RS25845 (C3F38_25840) | 35868..37217 | + | 1350 | WP_040119748 | conjugal transfer protein TraO | traO |
| C3F38_RS25850 (C3F38_25845) | 37229..37933 | + | 705 | WP_040119747 | conjugal transfer protein TraP | traP |
| C3F38_RS25855 (C3F38_25850) | 37957..38487 | + | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| C3F38_RS25860 (C3F38_25855) | 38504..38893 | + | 390 | WP_011091078 | DUF6750 family protein | traR |
| C3F38_RS25865 (C3F38_25860) | 38939..39433 | + | 495 | WP_011091080 | hypothetical protein | - |
| C3F38_RS25870 (C3F38_25865) | 39430..42480 | + | 3051 | WP_040119746 | conjugal transfer protein | traU |
| C3F38_RS25875 (C3F38_25870) | 42477..43685 | + | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| C3F38_RS25880 (C3F38_25875) | 43682..44278 | + | 597 | WP_015060003 | hypothetical protein | - |
| C3F38_RS25885 (C3F38_25880) | 44271..46466 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| C3F38_RS25890 (C3F38_25885) | 46468..47121 | + | 654 | WP_040119745 | hypothetical protein | - |
| C3F38_RS25895 (C3F38_25890) | 47203..47433 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
| C3F38_RS25900 (C3F38_25895) | 47730..48785 | + | 1056 | WP_015060006 | plasmid replication initiator RepA | - |
| C3F38_RS26790 | 50008..50103 | + | 96 | WP_004206884 | DinQ-like type I toxin DqlB | - |
Host bacterium
| ID | 14878 | GenBank | NZ_CP026385 |
| Plasmid name | pKPC-56ce | Incompatibility group | IncL/M |
| Plasmid size | 82860 bp | Coordinate of oriT [Strand] | 24252..24357 [+] |
| Host baterium | Serratia sp. SSNIH1 |
Cargo genes
| Drug resistance gene | blaKPC-2, blaSHV-12, qnrB19, aac(6')-Ib, ant(3'')-Ia, blaOXA-9, blaTEM-1A, ant(2'')-Ia |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |