Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113703 |
| Name | oriT_pB_CitB  |
| Organism | Citrobacter freundii strain CitB |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP048418 (33116..33221 [+], 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_pB_CitB
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8774 | GenBank | WP_171279082 |
| Name | Relaxase_GZ999_RS23635_pB_CitB |
UniProt ID | _ |
| Length | 659 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 659 a.a. Molecular weight: 75160.85 Da Isoelectric Point: 9.9601
>WP_171279082.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacteriaceae]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFEHDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFEHDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 10166 | GenBank | WP_171279081 |
| Name | t4cp2_GZ999_RS23385_pB_CitB |
UniProt ID | _ |
| Length | 695 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 695 a.a. Molecular weight: 79535.87 Da Isoelectric Point: 4.8309
>WP_171279081.1 MULTISPECIES: conjugal transfer protein TrbC [Enterobacteriaceae]
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVSFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMHFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVSFTDRKFRPPLR
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: 36017..55210
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| GZ999_RS23615 (GZ999_23605) | 31102..31413 | + | 312 | WP_015058934 | hypothetical protein | - |
| GZ999_RS23620 (GZ999_23610) | 31546..32082 | + | 537 | WP_015062822 | hypothetical protein | - |
| GZ999_RS23625 (GZ999_23615) | 32583..32978 | - | 396 | WP_019725163 | hypothetical protein | - |
| GZ999_RS23940 | 33013..33540 | + | 528 | WP_228298259 | plasmid mobilization protein MobA | - |
| GZ999_RS23635 (GZ999_23625) | 33527..35506 | + | 1980 | WP_171279082 | TraI/MobA(P) family conjugative relaxase | - |
| GZ999_RS23640 (GZ999_23630) | 35520..36020 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| GZ999_RS23645 (GZ999_23635) | 36017..36796 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| GZ999_RS23650 (GZ999_23640) | 36807..37970 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| GZ999_RS23655 (GZ999_23645) | 37960..38220 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| GZ999_RS23945 | 38245..41547 | + | 3303 | WP_228298260 | LPD7 domain-containing protein | - |
| GZ999_RS23665 (GZ999_23655) | 41513..42025 | + | 513 | WP_011091071 | hypothetical protein | traL |
| GZ999_RS23670 (GZ999_23660) | 42026..42238 | - | 213 | WP_305953721 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| GZ999_RS23675 (GZ999_23665) | 42210..42620 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| GZ999_RS23680 (GZ999_23670) | 42688..43401 | + | 714 | WP_228298261 | DotI/IcmL family type IV secretion protein | traM |
| GZ999_RS23685 (GZ999_23675) | 43410..44561 | + | 1152 | WP_011091074 | DotH/IcmK family type IV secretion protein | traN |
| GZ999_RS23690 (GZ999_23680) | 44573..45922 | + | 1350 | WP_015062830 | conjugal transfer protein TraO | traO |
| GZ999_RS23695 (GZ999_23685) | 45934..46638 | + | 705 | WP_045405147 | conjugal transfer protein TraP | traP |
| GZ999_RS23700 (GZ999_23690) | 46662..47192 | + | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| GZ999_RS23705 (GZ999_23695) | 47209..47598 | + | 390 | WP_015062832 | DUF6750 family protein | traR |
| GZ999_RS23710 (GZ999_23700) | 47644..48138 | + | 495 | WP_004187480 | hypothetical protein | - |
| GZ999_RS23715 (GZ999_23705) | 48135..51185 | + | 3051 | WP_045405150 | conjugal transfer protein | traU |
| GZ999_RS23720 (GZ999_23710) | 51182..52390 | + | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| GZ999_RS23725 (GZ999_23715) | 52387..53037 | + | 651 | WP_004187488 | hypothetical protein | - |
| GZ999_RS23730 (GZ999_23720) | 53030..55210 | + | 2181 | WP_004187492 | DotA/TraY family protein | traY |
| GZ999_RS23735 (GZ999_23725) | 55213..55866 | + | 654 | WP_045405152 | hypothetical protein | - |
| GZ999_RS23740 (GZ999_23730) | 55923..56171 | + | 249 | WP_015062836 | IncL/M type plasmid replication protein RepC | - |
Host bacterium
| ID | 14138 | GenBank | NZ_CP048418 |
| Plasmid name | pB_CitB | Incompatibility group | IncL/M |
| Plasmid size | 56468 bp | Coordinate of oriT [Strand] | 33116..33221 [+] |
| Host baterium | Citrobacter freundii strain CitB |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |