Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 116004 |
| Name | oriT_pIsolateH_B  |
| Organism | Citrobacter freundii strain isolateH |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP135467 (50654..50758 [+], 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_pIsolateH_B
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 10230 | GenBank | WP_004206924 |
| Name | traI_RRL14_RS24955_pIsolateH_B |
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 | 11953 | GenBank | WP_004206885 |
| Name | t4cp2_RRL14_RS24730_pIsolateH_B |
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: 53556..72752
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RRL14_RS24935 (RRL14_24935) | 48640..48951 | + | 312 | WP_004187333 | hypothetical protein | - |
| RRL14_RS24940 (RRL14_24940) | 49084..49620 | + | 537 | WP_004206920 | hypothetical protein | - |
| RRL14_RS24945 (RRL14_24945) | 50121..50486 | - | 366 | WP_004206922 | hypothetical protein | - |
| RRL14_RS24950 (RRL14_24950) | 50762..51079 | + | 318 | WP_004206923 | plasmid mobilization protein MobA | - |
| RRL14_RS24955 (RRL14_24955) | 51066..53045 | + | 1980 | WP_004206924 | TraI/MobA(P) family conjugative relaxase | - |
| RRL14_RS24960 (RRL14_24960) | 53059..53559 | + | 501 | WP_004206925 | DotD/TraH family lipoprotein | - |
| RRL14_RS24965 (RRL14_24965) | 53556..54335 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| RRL14_RS24970 (RRL14_24970) | 54346..55509 | + | 1164 | WP_004206926 | plasmid transfer ATPase TraJ | virB11 |
| RRL14_RS24975 (RRL14_24975) | 55499..55759 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| RRL14_RS24980 (RRL14_24980) | 55784..59089 | + | 3306 | WP_219818010 | LPD7 domain-containing protein | - |
| RRL14_RS24985 (RRL14_24985) | 59055..59567 | + | 513 | WP_011091071 | hypothetical protein | traL |
| RRL14_RS24990 (RRL14_24990) | 59568..59780 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| RRL14_RS24995 (RRL14_24995) | 59752..60162 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| RRL14_RS25000 (RRL14_25000) | 60230..60943 | + | 714 | WP_223294958 | DotI/IcmL family type IV secretion protein | traM |
| RRL14_RS25005 (RRL14_25005) | 60952..62103 | + | 1152 | WP_015062843 | DotH/IcmK family type IV secretion protein | traN |
| RRL14_RS25010 (RRL14_25010) | 62115..63464 | + | 1350 | WP_004206932 | conjugal transfer protein TraO | traO |
| RRL14_RS25015 (RRL14_25015) | 63476..64180 | + | 705 | WP_004206933 | conjugal transfer protein TraP | traP |
| RRL14_RS25020 (RRL14_25020) | 64204..64734 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| RRL14_RS25025 (RRL14_25025) | 64751..65140 | + | 390 | WP_011154472 | DUF6750 family protein | traR |
| RRL14_RS25030 (RRL14_25030) | 65186..65680 | + | 495 | WP_004187480 | hypothetical protein | - |
| RRL14_RS25035 (RRL14_25035) | 65677..68727 | + | 3051 | WP_011154474 | conjugative transfer protein | traU |
| RRL14_RS25040 (RRL14_25040) | 68724..69932 | + | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| RRL14_RS25045 (RRL14_25045) | 69929..70579 | + | 651 | WP_004187488 | hypothetical protein | - |
| RRL14_RS25050 (RRL14_25050) | 70572..72752 | + | 2181 | WP_004187492 | DotA/TraY family protein | traY |
| RRL14_RS25055 (RRL14_25055) | 72755..73408 | + | 654 | WP_004206935 | hypothetical protein | - |
| RRL14_RS25060 (RRL14_25060) | 73482..73712 | + | 231 | WP_004187496 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 16437 | GenBank | NZ_CP135467 |
| Plasmid name | pIsolateH_B | Incompatibility group | IncL/M |
| Plasmid size | 73996 bp | Coordinate of oriT [Strand] | 50654..50758 [+] |
| Host baterium | Citrobacter freundii strain isolateH |
Cargo genes
| Drug resistance gene | blaLAP-1, qnrS1, blaSHV-30 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |