Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 105845 |
| Name | oriT_pCCRI24236-3  |
| Organism | Citrobacter farmeri strain CCRI-24236 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP081317 (6663..6765 [-], 103 nt) |
| oriT length | 103 nt |
| IRs (inverted repeats) | 64..70, 73..79 (CCACCGT..ACGGTGG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 103 nt
>oriT_pCCRI24236-3
AGCCTCGCAGAGCAGGATTCCCGTTGAGCAGCCCAGCTGCGAATAAGGGAAGGTAAAGTTGGACCACCGTTTACGGTGGGCCTACTTTACATATCCTGCCCGG
AGCCTCGCAGAGCAGGATTCCCGTTGAGCAGCCCAGCTGCGAATAAGGGAAGGTAAAGTTGGACCACCGTTTACGGTGGGCCTACTTTACATATCCTGCCCGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3947 | GenBank | WP_050580356 |
| Name | Relaxase_Cf24236_RS25655_pCCRI24236-3 |
UniProt ID | _ |
| Length | 869 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 869 a.a. Molecular weight: 96507.42 Da Isoelectric Point: 10.4435
>WP_050580356.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacteriaceae]
MKNIKKSSFSGLADYITNPQSKQERVGVIKATNCQSQDVQDAVTEVNITQRLNTRSESDKTYHLVISFRP
GEKPSEDVLNAIEESICQSLGFGDHQRLSAVHHDTDNLHIHVAINKINPDTLTIHNPYNDYRVLAESCAY
LEKKYGLEVDNHMPTRSASENRAKDMERHSGIQSLLSWVKAECAEQLLNANSWQELHQAMRQNGLELRQK
GNGFVIAGPDGLAVKASSVDRSLSRAALEKKLGSFESSIPDTKPSRPSPEAIKQRFGSAANVKRPGDRPP
PMRENRQVHLGDVPVMQINSGKRYESKPLGSQGANTTELYGRYQSEQQRLTAARNEALRLAKVKRDRLIE
NAKRSGRLKRATIKLLKGPGVNKRYLYGLASKALGEELERANAIYKKDRQAAYDIHKRRTWADWLQFKAA
GGDDEALKTLRQRNAQQARKEANILHGDKVKKDGRIPGLKPDSVTKEGTIIYRVGESAIRDGGKRLDVSR
DAGDDGLHAALLMAKHRYGDKLTVNGSFEFKKRIVAVAAARELDVSFADPELEKLRQILTKKAAREREYI
HIPFEKRGKARQAGAMWDTEKKSWFVGPYATRDRIENFIRMNEEKDNEQRRQRYAGTERTDAGRERSGNG
NATGANEPGVTGRSTSADAGNGYGTSSSRRRTGTGDAVTTAGSQPGRSDDTRTGRSRAAEPNGERGHSKP
NVARPGRQPPPTAKNRLRAMSELGMVRIAGGSEVLLQGNVSDQLEHKTAERADQLRRDMAGAGGITTPAE
VKKPLSSAEKYINEREQKRLKGFDIPKHRGYNSTDKGLFEYAGQRKSGLETLALLKRDDEIVVMPVSDYT
ARRLSNLKVGESVTLTPSGSVRTTKGRSR
MKNIKKSSFSGLADYITNPQSKQERVGVIKATNCQSQDVQDAVTEVNITQRLNTRSESDKTYHLVISFRP
GEKPSEDVLNAIEESICQSLGFGDHQRLSAVHHDTDNLHIHVAINKINPDTLTIHNPYNDYRVLAESCAY
LEKKYGLEVDNHMPTRSASENRAKDMERHSGIQSLLSWVKAECAEQLLNANSWQELHQAMRQNGLELRQK
GNGFVIAGPDGLAVKASSVDRSLSRAALEKKLGSFESSIPDTKPSRPSPEAIKQRFGSAANVKRPGDRPP
PMRENRQVHLGDVPVMQINSGKRYESKPLGSQGANTTELYGRYQSEQQRLTAARNEALRLAKVKRDRLIE
NAKRSGRLKRATIKLLKGPGVNKRYLYGLASKALGEELERANAIYKKDRQAAYDIHKRRTWADWLQFKAA
GGDDEALKTLRQRNAQQARKEANILHGDKVKKDGRIPGLKPDSVTKEGTIIYRVGESAIRDGGKRLDVSR
DAGDDGLHAALLMAKHRYGDKLTVNGSFEFKKRIVAVAAARELDVSFADPELEKLRQILTKKAAREREYI
HIPFEKRGKARQAGAMWDTEKKSWFVGPYATRDRIENFIRMNEEKDNEQRRQRYAGTERTDAGRERSGNG
NATGANEPGVTGRSTSADAGNGYGTSSSRRRTGTGDAVTTAGSQPGRSDDTRTGRSRAAEPNGERGHSKP
NVARPGRQPPPTAKNRLRAMSELGMVRIAGGSEVLLQGNVSDQLEHKTAERADQLRRDMAGAGGITTPAE
VKKPLSSAEKYINEREQKRLKGFDIPKHRGYNSTDKGLFEYAGQRKSGLETLALLKRDDEIVVMPVSDYT
ARRLSNLKVGESVTLTPSGSVRTTKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 3963 | GenBank | WP_024252940 |
| Name | t4cp2_Cf24236_RS25665_pCCRI24236-3 |
UniProt ID | _ |
| Length | 648 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 648 a.a. Molecular weight: 71684.76 Da Isoelectric Point: 8.1395
>WP_024252940.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MRKPNNAVGPQVRNKKKTARGKLIPAMAITSLAAGIQAATQYFAYSFNYQELLGPNFNHIYAPWSYFKWY
SAWHDRLPDAFFAAGSVGATVAAGGLVLTALTSMMKANSSKANEYLHGSARWADEQDIKAAGLLGNDEGV
YVGAWEDKNGQLQYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWKHSTVVADLKGELWAMTAGWRKEYA
KNLCLKFEPAAANGSVAWNPLDEIRVGTENEVGDVQNLATLIVDPDGKGLNDHWQKTSQALLVGVILHVL
YKHKNDGTPATLPYVDSIMADPERGAGELWMEMTQYGHVNGENHPVVGAAGRDMMDRPEEEAGSVLSTAK
SYLALFRDPVVARNVSESHFKIKDLMNHDDPVSLYIVTQPNDKARLRPLVRIMLNMIVRLLADKMEFERV
NNNLTLWQRFKQAFGFSVQGTKRVQTKKTYKHRLLAMIDEFPSLGKLEIIQESLAFLAGYGIKFYLICQD
INQLRSRETGYGPDETITSNCHVQNAYPPNRTETAEHLSKLTGQTTVIKEQITTSGKRASAILGGVSKTM
QEVQRPLLTVDECLRMPGPTKNAEGLITERGDMVVYVAGFPAIYGKQPLFFQDEIFSLRASVPEPKTTDR
IRAAVAANDDASNEAIAI
MRKPNNAVGPQVRNKKKTARGKLIPAMAITSLAAGIQAATQYFAYSFNYQELLGPNFNHIYAPWSYFKWY
SAWHDRLPDAFFAAGSVGATVAAGGLVLTALTSMMKANSSKANEYLHGSARWADEQDIKAAGLLGNDEGV
YVGAWEDKNGQLQYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWKHSTVVADLKGELWAMTAGWRKEYA
KNLCLKFEPAAANGSVAWNPLDEIRVGTENEVGDVQNLATLIVDPDGKGLNDHWQKTSQALLVGVILHVL
YKHKNDGTPATLPYVDSIMADPERGAGELWMEMTQYGHVNGENHPVVGAAGRDMMDRPEEEAGSVLSTAK
SYLALFRDPVVARNVSESHFKIKDLMNHDDPVSLYIVTQPNDKARLRPLVRIMLNMIVRLLADKMEFERV
NNNLTLWQRFKQAFGFSVQGTKRVQTKKTYKHRLLAMIDEFPSLGKLEIIQESLAFLAGYGIKFYLICQD
INQLRSRETGYGPDETITSNCHVQNAYPPNRTETAEHLSKLTGQTTVIKEQITTSGKRASAILGGVSKTM
QEVQRPLLTVDECLRMPGPTKNAEGLITERGDMVVYVAGFPAIYGKQPLFFQDEIFSLRASVPEPKTTDR
IRAAVAANDDASNEAIAI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 30133..40445
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Cf24236_RS25760 (Cf24236_7033) | 25458..26093 | + | 636 | WP_024252949 | recombinase family protein | - |
| Cf24236_RS25765 (Cf24236_7034) | 26083..26613 | + | 531 | WP_024252950 | thermonuclease family protein | - |
| Cf24236_RS25770 (Cf24236_7035) | 26766..26996 | + | 231 | WP_024252951 | hypothetical protein | - |
| Cf24236_RS25775 (Cf24236_7036) | 27399..27719 | + | 321 | WP_024252952 | hypothetical protein | - |
| Cf24236_RS26465 | 27780..27875 | - | 96 | WP_003019619 | DinQ-like type I toxin DqlB | - |
| Cf24236_RS25780 (Cf24236_7037) | 28328..29014 | - | 687 | WP_024252953 | TraX family protein | - |
| Cf24236_RS25785 (Cf24236_7038) | 29031..29801 | - | 771 | WP_024252954 | conjugal transfer protein | - |
| Cf24236_RS25790 (Cf24236_7039) | 29817..30122 | - | 306 | WP_003019624 | IncN plasmid KikA protein | - |
| Cf24236_RS25795 (Cf24236_7040) | 30133..31686 | - | 1554 | WP_024252955 | P-type conjugative transfer protein TrbL | virB6 |
| Cf24236_RS25800 (Cf24236_7041) | 31691..31864 | - | 174 | WP_024252956 | entry exclusion lipoprotein TrbK | - |
| Cf24236_RS25805 (Cf24236_7042) | 31877..32647 | - | 771 | WP_004196177 | P-type conjugative transfer protein TrbJ | virB5 |
| Cf24236_RS25810 (Cf24236_7043) | 32660..34054 | - | 1395 | WP_024252958 | TrbI/VirB10 family protein | virB10 |
| Cf24236_RS25815 (Cf24236_7044) | 34058..34510 | - | 453 | WP_032194780 | conjugal transfer protein TrbH | - |
| Cf24236_RS25820 (Cf24236_7045) | 34513..35403 | - | 891 | WP_024252960 | P-type conjugative transfer protein TrbG | virB9 |
| Cf24236_RS25825 (Cf24236_7046) | 35419..36126 | - | 708 | WP_024252961 | VirB8/TrbF family protein | virB8 |
| Cf24236_RS25830 (Cf24236_7047) | 36123..38666 | - | 2544 | WP_024252962 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| Cf24236_RS25835 (Cf24236_7048) | 38663..38989 | - | 327 | WP_024252963 | conjugal transfer protein TrbD | virB3 |
| Cf24236_RS25840 (Cf24236_7049) | 38992..39375 | - | 384 | WP_024252964 | TrbC/VirB2 family protein | virB2 |
| Cf24236_RS25845 (Cf24236_7050) | 39489..40445 | - | 957 | WP_024269749 | P-type conjugative transfer ATPase TrbB | virB11 |
| Cf24236_RS25850 (Cf24236_7051) | 40630..41034 | - | 405 | WP_024252966 | transcriptional regulator | - |
| Cf24236_RS25855 (Cf24236_7052) | 41140..41511 | + | 372 | WP_024252967 | single-stranded DNA-binding protein | - |
| Cf24236_RS25860 (Cf24236_7053) | 41592..42470 | + | 879 | WP_032194784 | plasmid replication initiator TrfA | - |
| Cf24236_RS25865 (Cf24236_7054) | 43483..43782 | + | 300 | WP_222563852 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| Cf24236_RS25870 (Cf24236_7055) | 43791..44099 | + | 309 | WP_003019666 | HigA family addiction module antitoxin | - |
| Cf24236_RS25875 (Cf24236_7056) | 44099..44347 | + | 249 | WP_024252919 | antirestriction protein ArdR | - |
| Cf24236_RS25880 (Cf24236_7057) | 44344..44928 | + | 585 | WP_024252920 | hypothetical protein | - |
| Cf24236_RS25885 (Cf24236_7058) | 45018..45215 | + | 198 | WP_024252921 | DUF905 family protein | - |
Host bacterium
| ID | 6282 | GenBank | NZ_CP081317 |
| Plasmid name | pCCRI24236-3 | Incompatibility group | IncP1 |
| Plasmid size | 52406 bp | Coordinate of oriT [Strand] | 6663..6765 [-] |
| Host baterium | Citrobacter farmeri strain CCRI-24236 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |