Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120428 |
| Name | oriT_p24A17004_B_KPC  |
| Organism | Citrobacter freundii strain 24A17CRGN004 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OQ821125 (48846..48951 [+], 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_p24A17004_B_KPC
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12864 | GenBank | WP_004187323 |
| Name | traI_SLH58_RS00335_p24A17004_B_KPC |
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 | 15112 | GenBank | WP_038874906 |
| Name | t4cp2_SLH58_RS00060_p24A17004_B_KPC |
UniProt ID | _ |
| Length | 701 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 701 a.a. Molecular weight: 80068.49 Da Isoelectric Point: 4.8705
>WP_038874906.1 MULTISPECIES: conjugal transfer protein TrbC [Enterobacterales]
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAESNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIGVVSEFG
K
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAESNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIGVVSEFG
K
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 51747..71075
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SLH58_RS00315 (LBOALNMF_00061) | 46833..47144 | + | 312 | WP_004187333 | hypothetical protein | - |
| SLH58_RS00320 (LBOALNMF_00062) | 47276..47812 | + | 537 | WP_011091066 | hypothetical protein | - |
| SLH58_RS00325 (LBOALNMF_00064) | 48313..48708 | - | 396 | WP_020805633 | hypothetical protein | - |
| SLH58_RS00330 | 48707..49270 | + | 564 | WP_319382137 | plasmid mobilization protein MobA | - |
| SLH58_RS00335 (LBOALNMF_00066) | 49257..51236 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| SLH58_RS00340 (LBOALNMF_00067) | 51250..51750 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| SLH58_RS00345 (LBOALNMF_00068) | 51747..52526 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| SLH58_RS00350 (LBOALNMF_00069) | 52537..53700 | + | 1164 | WP_020805653 | plasmid transfer ATPase TraJ | virB11 |
| SLH58_RS00355 (LBOALNMF_00070) | 53690..53950 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| SLH58_RS00360 (LBOALNMF_00071) | 53975..57412 | + | 3438 | WP_319382138 | LPD7 domain-containing protein | - |
| SLH58_RS00365 (LBOALNMF_00072) | 57336..57890 | + | 555 | WP_011154467 | hypothetical protein | traL |
| SLH58_RS00370 (LBOALNMF_00073) | 57891..58088 | - | 198 | WP_004187464 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| SLH58_RS00375 (LBOALNMF_00074) | 58075..58485 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| SLH58_RS00380 (LBOALNMF_00075) | 58484..59266 | + | 783 | WP_004206929 | DotI/IcmL family type IV secretion protein | traM |
| SLH58_RS00385 (LBOALNMF_00076) | 59302..60426 | + | 1125 | WP_319382139 | DotH/IcmK family type IV secretion protein | traN |
| SLH58_RS00390 (LBOALNMF_00077) | 60438..61787 | + | 1350 | WP_020805691 | conjugal transfer protein TraO | traO |
| SLH58_RS00395 (LBOALNMF_00078) | 61799..62503 | + | 705 | WP_020805696 | conjugal transfer protein TraP | traP |
| SLH58_RS00400 (LBOALNMF_00079) | 62527..63057 | + | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| SLH58_RS00405 (LBOALNMF_00080) | 63074..63463 | + | 390 | WP_020805690 | DUF6750 family protein | traR |
| SLH58_RS00410 (LBOALNMF_00081) | 63509..64003 | + | 495 | WP_223294957 | hypothetical protein | - |
| SLH58_RS00415 (LBOALNMF_00082) | 64000..67050 | + | 3051 | WP_020805687 | ATPase AAA | traU |
| SLH58_RS00420 (LBOALNMF_00083) | 67080..68255 | + | 1176 | WP_167577398 | conjugal transfer protein TraW | traW |
| SLH58_RS00425 (LBOALNMF_00084) | 68252..68902 | + | 651 | WP_032426814 | hypothetical protein | - |
| SLH58_RS00430 (LBOALNMF_00085) | 68895..71075 | + | 2181 | WP_032426815 | DotA/TraY family protein | traY |
| SLH58_RS00435 (LBOALNMF_00086) | 71078..71731 | + | 654 | WP_020805693 | hypothetical protein | - |
| SLH58_RS00440 (LBOALNMF_00087) | 71793..72035 | + | 243 | WP_023893611 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 20857 | GenBank | NZ_OQ821125 |
| Plasmid name | p24A17004_B_KPC | Incompatibility group | IncL/M |
| Plasmid size | 72331 bp | Coordinate of oriT [Strand] | 48846..48951 [+] |
| Host baterium | Citrobacter freundii strain 24A17CRGN004 |
Cargo genes
| Drug resistance gene | blaKPC-3 |
| Virulence gene | - |
| Metal resistance gene | merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |