Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 116536 |
| Name | oriT_pF2119-3  |
| Organism | Citrobacter freundii strain F2119 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP137116 (35073..35178 [+], 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_pF2119-3
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 10558 | GenBank | WP_004187323 |
| Name | traI_R2X26_RS00275_pF2119-3 |
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 | 12341 | GenBank | WP_004187443 |
| Name | t4cp2_R2X26_RS00015_pF2119-3 |
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: 37974..57263
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| R2X26_RS00255 (R2X26_00255) | 33058..33369 | + | 312 | WP_004187333 | hypothetical protein | - |
| R2X26_RS00260 (R2X26_00260) | 33502..34038 | + | 537 | WP_004187332 | hypothetical protein | - |
| R2X26_RS00265 (R2X26_00265) | 34540..34935 | - | 396 | WP_019725163 | hypothetical protein | - |
| R2X26_RS00270 (R2X26_00270) | 34970..35497 | + | 528 | WP_172740549 | plasmid mobilization protein MobA | - |
| R2X26_RS00275 (R2X26_00275) | 35484..37463 | + | 1980 | WP_004187323 | TraI/MobA(P) family conjugative relaxase | - |
| R2X26_RS00280 (R2X26_00280) | 37477..37977 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| R2X26_RS00285 (R2X26_00285) | 37974..38753 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| R2X26_RS00290 (R2X26_00290) | 38764..39927 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| R2X26_RS00295 (R2X26_00295) | 39917..40177 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| R2X26_RS00300 (R2X26_00300) | 40202..43639 | + | 3438 | WP_317810987 | LPD7 domain-containing protein | - |
| R2X26_RS00305 (R2X26_00305) | 43605..44117 | + | 513 | WP_011091071 | hypothetical protein | traL |
| R2X26_RS00310 (R2X26_00310) | 44118..44330 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| R2X26_RS00315 (R2X26_00315) | 44302..44712 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| R2X26_RS00320 (R2X26_00320) | 44780..45493 | + | 714 | WP_004187467 | DotI/IcmL family type IV secretion protein | traM |
| R2X26_RS00325 (R2X26_00325) | 45502..46653 | + | 1152 | WP_004187471 | DotH/IcmK family type IV secretion protein | traN |
| R2X26_RS00330 (R2X26_00330) | 46665..48014 | + | 1350 | WP_004187474 | conjugal transfer protein TraO | traO |
| R2X26_RS00335 (R2X26_00335) | 48026..48730 | + | 705 | WP_015060002 | conjugal transfer protein TraP | traP |
| R2X26_RS00340 (R2X26_00340) | 48754..49284 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| R2X26_RS00345 (R2X26_00345) | 49301..49690 | + | 390 | WP_004187479 | DUF6750 family protein | traR |
| R2X26_RS00350 (R2X26_00350) | 49736..50230 | + | 495 | WP_004187480 | hypothetical protein | - |
| R2X26_RS00355 (R2X26_00355) | 50227..53277 | + | 3051 | WP_004187482 | hypothetical protein | traU |
| R2X26_RS00360 (R2X26_00360) | 53274..54482 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| R2X26_RS00365 (R2X26_00365) | 54479..55075 | + | 597 | WP_015060003 | hypothetical protein | - |
| R2X26_RS00370 (R2X26_00370) | 55068..57263 | + | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| R2X26_RS00375 (R2X26_00375) | 57265..57918 | + | 654 | WP_044706695 | hypothetical protein | - |
| R2X26_RS00380 (R2X26_00380) | 57999..58229 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 16969 | GenBank | NZ_CP137116 |
| Plasmid name | pF2119-3 | Incompatibility group | IncL/M |
| Plasmid size | 58524 bp | Coordinate of oriT [Strand] | 35073..35178 [+] |
| Host baterium | Citrobacter freundii strain F2119 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |