Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103528 |
| Name | oriT_402|P1  |
| Organism | Citrobacter freundii isolate 402 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OW849100 (51029..51134 [+], 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_402|P1
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2641 | GenBank | WP_004187323 |
| Name | Relaxase_LQ100_RS23600_402|P1 |
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 | 2450 | GenBank | WP_004206885 |
| Name | t4cp2_LQ100_RS23220_402|P1 |
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: 53930..73219
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| LQ100_RS23580 (AI2609V1_4574) | 49014..49325 | + | 312 | WP_004187333 | hypothetical protein | - |
| LQ100_RS23585 (AI2609V1_4575) | 49458..49994 | + | 537 | WP_004187332 | hypothetical protein | - |
| LQ100_RS23590 (AI2609V1_4577) | 50496..50891 | - | 396 | WP_019725163 | hypothetical protein | - |
| LQ100_RS23595 | 50926..51453 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| LQ100_RS23600 (AI2609V1_4579) | 51440..53419 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| LQ100_RS23605 (AI2609V1_4580) | 53433..53933 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| LQ100_RS23610 (AI2609V1_4581) | 53930..54709 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| LQ100_RS23615 (AI2609V1_4582) | 54720..55883 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| LQ100_RS23620 (AI2609V1_4583) | 55873..56133 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| LQ100_RS23625 (AI2609V1_4584) | 56158..59595 | + | 3438 | WP_225373171 | LPD7 domain-containing protein | - |
| LQ100_RS23630 (AI2609V1_4585) | 59561..60073 | + | 513 | WP_011091071 | hypothetical protein | traL |
| LQ100_RS23635 (AI2609V1_4586) | 60074..60286 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| LQ100_RS23640 (AI2609V1_4587) | 60258..60668 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| LQ100_RS23645 (AI2609V1_4588) | 60736..61449 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| LQ100_RS23650 (AI2609V1_4589) | 61458..62609 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| LQ100_RS23655 (AI2609V1_4590) | 62621..63970 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| LQ100_RS23660 (AI2609V1_4591) | 63982..64686 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| LQ100_RS23665 (AI2609V1_4592) | 64710..65240 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| LQ100_RS23670 (AI2609V1_4593) | 65257..65646 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| LQ100_RS23675 (AI2609V1_4594) | 65692..66186 | + | 495 | WP_004187480 | hypothetical protein | - |
| LQ100_RS23680 (AI2609V1_4595) | 66183..69233 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| LQ100_RS23685 (AI2609V1_4596) | 69230..70438 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| LQ100_RS23690 (AI2609V1_4597) | 70435..71031 | + | 597 | WP_015060003 | hypothetical protein | - |
| LQ100_RS23695 (AI2609V1_4598) | 71024..73219 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| LQ100_RS23700 (AI2609V1_4599) | 73221..73874 | + | 654 | WP_015060005 | hypothetical protein | - |
| LQ100_RS23705 (AI2609V1_4600) | 73955..74185 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 3971 | GenBank | NZ_OW849100 |
| Plasmid name | 402|P1 | Incompatibility group | IncL/M |
| Plasmid size | 74480 bp | Coordinate of oriT [Strand] | 51029..51134 [+] |
| Host baterium | Citrobacter freundii isolate 402 |
Cargo genes
| Drug resistance gene | catA1, blaVIM-1, dfrB1, ant(3'')-Ia, catB2, qacE, sul1, qnrB2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |