Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120492 |
| Name | oriT_pKPC_CAV1857-85  |
| Organism | Citrobacter freundii strain CAV1857 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP037737 (47256..47360 [+], 105 nt) |
| oriT length | 105 nt |
| IRs (inverted repeats) | 32..37, 40..45 (GCCGGC..GCCGGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 105 nt
>oriT_pKPC_CAV1857-85
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12904 | GenBank | WP_004206924 |
| Name | traI_E1A41_RS26415_pKPC_CAV1857-85 |
UniProt ID | A0A2V4FJ40 |
| Length | 659 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 659 a.a. Molecular weight: 75087.84 Da Isoelectric Point: 10.0285
>WP_004206924.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFAGIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQLRSESDDKFNPK
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFAGIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQLRSESDDKFNPK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A2V4FJ40 |
T4CP
| ID | 15155 | GenBank | WP_004206885 |
| Name | t4cp2_E1A41_RS26165_pKPC_CAV1857-85 |
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: 50158..66534
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| E1A41_RS26395 (E1A41_26395) | 45242..45553 | + | 312 | WP_004187333 | hypothetical protein | - |
| E1A41_RS26400 (E1A41_26400) | 45686..46222 | + | 537 | WP_004206920 | hypothetical protein | - |
| E1A41_RS26405 (E1A41_26405) | 46723..47088 | - | 366 | WP_004206922 | hypothetical protein | - |
| E1A41_RS26410 (E1A41_26410) | 47364..47681 | + | 318 | WP_004206923 | plasmid mobilization protein MobA | - |
| E1A41_RS26415 (E1A41_26415) | 47668..49647 | + | 1980 | WP_004206924 | TraI/MobA(P) family conjugative relaxase | - |
| E1A41_RS26420 (E1A41_26420) | 49661..50161 | + | 501 | WP_004206925 | DotD/TraH family lipoprotein | - |
| E1A41_RS26425 (E1A41_26425) | 50158..50937 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| E1A41_RS26430 (E1A41_26430) | 50948..52111 | + | 1164 | WP_004206926 | plasmid transfer ATPase TraJ | virB11 |
| E1A41_RS26435 (E1A41_26435) | 52101..52361 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| E1A41_RS27635 | 52386..55691 | + | 3306 | WP_219818010 | LPD7 domain-containing protein | - |
| E1A41_RS26445 (E1A41_26445) | 55657..56169 | + | 513 | WP_011091071 | hypothetical protein | traL |
| E1A41_RS26450 (E1A41_26450) | 56170..56382 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| E1A41_RS26455 (E1A41_26455) | 56354..56764 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| E1A41_RS26460 (E1A41_26460) | 56832..57545 | + | 714 | WP_223294958 | DotI/IcmL family type IV secretion protein | traM |
| E1A41_RS26465 (E1A41_26465) | 57554..58705 | + | 1152 | WP_015062843 | DotH/IcmK family type IV secretion protein | traN |
| E1A41_RS26470 (E1A41_26470) | 58717..60066 | + | 1350 | WP_004206932 | conjugal transfer protein TraO | traO |
| E1A41_RS26475 (E1A41_26475) | 60078..60782 | + | 705 | WP_004206933 | conjugal transfer protein TraP | traP |
| E1A41_RS26480 (E1A41_26480) | 60806..61336 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| E1A41_RS26485 (E1A41_26485) | 61353..61742 | + | 390 | WP_011154472 | DUF6750 family protein | traR |
| E1A41_RS26490 (E1A41_26490) | 61788..62282 | + | 495 | WP_004187480 | hypothetical protein | - |
| E1A41_RS26495 (E1A41_26495) | 62279..65329 | + | 3051 | WP_011154474 | conjugative transfer protein | traU |
| E1A41_RS26500 (E1A41_26500) | 65326..66534 | + | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| E1A41_RS26505 (E1A41_26505) | 66531..67181 | + | 651 | WP_004187488 | hypothetical protein | - |
| E1A41_RS27755 (E1A41_26510) | 67297..67707 | + | 411 | Protein_84 | DotA/TraY family protein | - |
| E1A41_RS26515 (E1A41_26515) | 67784..69862 | - | 2079 | Protein_85 | Tn3-like element Tn3 family transposase | - |
Host bacterium
| ID | 20921 | GenBank | NZ_CP037737 |
| Plasmid name | pKPC_CAV1857-85 | Incompatibility group | IncL/M |
| Plasmid size | 85575 bp | Coordinate of oriT [Strand] | 47256..47360 [+] |
| Host baterium | Citrobacter freundii strain CAV1857 |
Cargo genes
| Drug resistance gene | ant(3'')-Ia, qacE, sul1, blaSHV-30, blaKPC-2, blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |