Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120563 |
| Name | oriT_pMB3888B_2  |
| Organism | Klebsiella oxytoca strain ST34 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP103692 (23150..23254 [+], 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_pMB3888B_2
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12953 | GenBank | WP_004206924 |
| Name | traI_M5T43_RS30255_pMB3888B_2 |
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 | 15208 | GenBank | WP_004206885 |
| Name | t4cp2_M5T43_RS30440_pMB3888B_2 |
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: 26052..45248
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| M5T43_RS30235 (M5T43_30235) | 21136..21447 | + | 312 | WP_004187333 | hypothetical protein | - |
| M5T43_RS30240 (M5T43_30240) | 21580..22116 | + | 537 | WP_004206920 | hypothetical protein | - |
| M5T43_RS30245 (M5T43_30245) | 22617..22982 | - | 366 | WP_004206922 | hypothetical protein | - |
| M5T43_RS30250 (M5T43_30250) | 23258..23575 | + | 318 | WP_004206923 | plasmid mobilization protein MobA | - |
| M5T43_RS30255 (M5T43_30255) | 23562..25541 | + | 1980 | WP_004206924 | TraI/MobA(P) family conjugative relaxase | - |
| M5T43_RS30260 (M5T43_30260) | 25555..26055 | + | 501 | WP_004206925 | DotD/TraH family lipoprotein | - |
| M5T43_RS30265 (M5T43_30265) | 26052..26831 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| M5T43_RS30270 (M5T43_30270) | 26842..28005 | + | 1164 | WP_004206926 | plasmid transfer ATPase TraJ | virB11 |
| M5T43_RS30275 (M5T43_30275) | 27995..28255 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| M5T43_RS30280 (M5T43_30280) | 28280..31585 | + | 3306 | WP_219818010 | LPD7 domain-containing protein | - |
| M5T43_RS30285 (M5T43_30285) | 31551..32063 | + | 513 | WP_011091071 | hypothetical protein | traL |
| M5T43_RS30290 (M5T43_30290) | 32064..32276 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| M5T43_RS30295 (M5T43_30295) | 32248..32658 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| M5T43_RS30300 (M5T43_30300) | 32726..33439 | + | 714 | WP_223294958 | DotI/IcmL family type IV secretion protein | traM |
| M5T43_RS30305 (M5T43_30305) | 33448..34599 | + | 1152 | WP_015062843 | DotH/IcmK family type IV secretion protein | traN |
| M5T43_RS30310 (M5T43_30310) | 34611..35960 | + | 1350 | WP_004206932 | conjugal transfer protein TraO | traO |
| M5T43_RS30315 (M5T43_30315) | 35972..36676 | + | 705 | WP_004206933 | conjugal transfer protein TraP | traP |
| M5T43_RS30320 (M5T43_30320) | 36700..37230 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| M5T43_RS30325 (M5T43_30325) | 37247..37636 | + | 390 | WP_011154472 | DUF6750 family protein | traR |
| M5T43_RS30330 (M5T43_30330) | 37682..38176 | + | 495 | WP_004187480 | hypothetical protein | - |
| M5T43_RS30335 (M5T43_30335) | 38173..41223 | + | 3051 | WP_011154474 | conjugative transfer protein | traU |
| M5T43_RS30340 (M5T43_30340) | 41220..42428 | + | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| M5T43_RS30345 (M5T43_30345) | 42425..43075 | + | 651 | WP_004187488 | hypothetical protein | - |
| M5T43_RS30350 (M5T43_30350) | 43068..45248 | + | 2181 | WP_004187492 | DotA/TraY family protein | traY |
| M5T43_RS30355 (M5T43_30355) | 45251..45904 | + | 654 | WP_004206935 | hypothetical protein | - |
| M5T43_RS30360 (M5T43_30360) | 45978..46208 | + | 231 | WP_004187496 | IncL/M type plasmid replication protein RepC | - |
| M5T43_RS30365 (M5T43_30365) | 46505..47560 | + | 1056 | WP_015062846 | plasmid replication initiator RepA | - |
| M5T43_RS30370 (M5T43_30370) | 48732..49265 | - | 534 | Protein_54 | IS110-like element IS4321 family transposase | - |
Host bacterium
| ID | 20992 | GenBank | NZ_CP103692 |
| Plasmid name | pMB3888B_2 | Incompatibility group | IncL/M |
| Plasmid size | 81842 bp | Coordinate of oriT [Strand] | 23150..23254 [+] |
| Host baterium | Klebsiella oxytoca strain ST34 |
Cargo genes
| Drug resistance gene | blaKPC-2, ant(2'')-Ia, blaSHV-30, qnrS1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |