Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 105262 |
| Name | oriT_pRHBSTW-00488_5  |
| Organism | Citrobacter freundii strain RHBSTW-00488 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP055470 (3033..3627 [-], 595 nt) |
| oriT length | 595 nt |
| IRs (inverted repeats) | 569..574, 579..584 (ATGCCC..GGGCAT) 497..503, 508..514 (CCTCCCG..CGGGAGG) 433..438, 442..447 (GTTCGC..GCGAAC) 75..80, 86..91 (TGCTTT..AAAGCA) 69..74, 82..87 (TTACTT..AAGTAA) |
| Location of nic site | 294..295 |
| Conserved sequence flanking the nic site |
TCCTGCATCG |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 595 nt
>oriT_pRHBSTW-00488_5
TGTTAAATACATTGTAGTTTTGATAAAATCATTAGTATCTGGCATAAAGTTATCATTATCATCTTCTGTTACTTTGCTTTTAAGTAAAGCACTGGCAAGCAATTTCATGCCTTTAGCAACAGTTAAACCAGGCTCATCTGGATAAATAACCTTCAGACATTCAAGTAGATTATCATGCTGTTTTTCTTCTAGTCTGAAATTAATTTGCTTCATAAATCCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGAGTAAAATGCTAGCATTTTGCGGCGTTTGCCCTATCCTGCATCGCTTTGATCTAGCACTAGTCTTGAATTGTGCTTCAGCGTCGAGGAAAAAGCAAAACTGAAGGGCTGTCATGGCTGAAGGTTTCGCTTGTCTACGACCGGAAACATCTCAATGGCTGTGAGCTATGTGGGATAAGGTTCGCTACGCGAACGGTCTGGCAGGGGGCGCAAGCGCTGTCTTGCAGAGTATATAAAAAAGCACCTCCCGCAAACGGGAGGGCTTCGGCGATTCATGACGTGTGAAACTATTCAGGGTCTGGTGTGTCGCCTACCATGCCCTGACGGGCATCACACAACCAG
TGTTAAATACATTGTAGTTTTGATAAAATCATTAGTATCTGGCATAAAGTTATCATTATCATCTTCTGTTACTTTGCTTTTAAGTAAAGCACTGGCAAGCAATTTCATGCCTTTAGCAACAGTTAAACCAGGCTCATCTGGATAAATAACCTTCAGACATTCAAGTAGATTATCATGCTGTTTTTCTTCTAGTCTGAAATTAATTTGCTTCATAAATCCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGAGTAAAATGCTAGCATTTTGCGGCGTTTGCCCTATCCTGCATCGCTTTGATCTAGCACTAGTCTTGAATTGTGCTTCAGCGTCGAGGAAAAAGCAAAACTGAAGGGCTGTCATGGCTGAAGGTTTCGCTTGTCTACGACCGGAAACATCTCAATGGCTGTGAGCTATGTGGGATAAGGTTCGCTACGCGAACGGTCTGGCAGGGGGCGCAAGCGCTGTCTTGCAGAGTATATAAAAAAGCACCTCCCGCAAACGGGAGGGCTTCGGCGATTCATGACGTGTGAAACTATTCAGGGTCTGGTGTGTCGCCTACCATGCCCTGACGGGCATCACACAACCAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3607 | GenBank | WP_044715149 |
| Name | mobP1_HV215_RS25405_pRHBSTW-00488_5 |
UniProt ID | A0A2L1K6C2 |
| Length | 386 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 386 a.a. Molecular weight: 44400.90 Da Isoelectric Point: 10.6126
>WP_044715149.1 MULTISPECIES: MobP1 family relaxase [Enterobacterales]
MGVSVDKEYRFKRKSSEAGRKSAFAHKVKNGGKNYQRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGQVWKGDEIQEAKEHMVDRANDPQNVMNDKGKENKKVTQNIVFSPPVSAKVKPED
LLESVRKTMHKKYPNHRFVLGYHNDKKDHPHVHVVFRIRDEDGKRTDIRKKDLREIRTGFCEELKLKGYD
VKATHRQQQGLNQSIRDAHSTAPKRQKGVYEVVDVGYDHYQHDKTKPKQHFLKLKTLNKGVEKTYWGADF
GDLTSRENVKKGDLVKLKKLGQKEVKIPALDKHGVQHGWKTVHRNEWKLDNLGVKGIDRTPSSSKELVLN
SAAMLQKQQLQMKQFIQIKQAMLQNEQKMKIGIKLG
MGVSVDKEYRFKRKSSEAGRKSAFAHKVKNGGKNYQRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGQVWKGDEIQEAKEHMVDRANDPQNVMNDKGKENKKVTQNIVFSPPVSAKVKPED
LLESVRKTMHKKYPNHRFVLGYHNDKKDHPHVHVVFRIRDEDGKRTDIRKKDLREIRTGFCEELKLKGYD
VKATHRQQQGLNQSIRDAHSTAPKRQKGVYEVVDVGYDHYQHDKTKPKQHFLKLKTLNKGVEKTYWGADF
GDLTSRENVKKGDLVKLKKLGQKEVKIPALDKHGVQHGWKTVHRNEWKLDNLGVKGIDRTPSSSKELVLN
SAAMLQKQQLQMKQFIQIKQAMLQNEQKMKIGIKLG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A2L1K6C2 |
T4CP
| ID | 3570 | GenBank | WP_044715174 |
| Name | t4cp2_HV215_RS25465_pRHBSTW-00488_5 |
UniProt ID | _ |
| Length | 611 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 611 a.a. Molecular weight: 69245.98 Da Isoelectric Point: 7.1493
>WP_044715174.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacterales]
MSLKLPDKGQWLFIGFVMCLFTYYAGSVAVYFFNGKTPLFIWKNFDSMLLWRLMTESNIRSDIRITAMPA
LLSGLAASVIVPVFIIWQLNKKDFSLYGDAKFASDDDLKKSKLLKWEKENDDDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREVILQNKVFLLDPFNSKTHKFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYAPDWLNEFNLKPIFSI
GSVVDLYSNIDRENVLANREDFEGIAGLDETALFHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDISIYVGVNAEDMSLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAKKIS
EKLGYTTAKSTGSSKTSGRSTSKSNSESDAQRALVLPQELGTLEFSEEFIILKGENPVKAKKALYYLDSY
FMDRLMLVSPKLAALTSSLNKTKNIFGVKGLKYPSKEKMLSVGELESEVLL
MSLKLPDKGQWLFIGFVMCLFTYYAGSVAVYFFNGKTPLFIWKNFDSMLLWRLMTESNIRSDIRITAMPA
LLSGLAASVIVPVFIIWQLNKKDFSLYGDAKFASDDDLKKSKLLKWEKENDDDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREVILQNKVFLLDPFNSKTHKFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYAPDWLNEFNLKPIFSI
GSVVDLYSNIDRENVLANREDFEGIAGLDETALFHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDISIYVGVNAEDMSLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAKKIS
EKLGYTTAKSTGSSKTSGRSTSKSNSESDAQRALVLPQELGTLEFSEEFIILKGENPVKAKKALYYLDSY
FMDRLMLVSPKLAALTSSLNKTKNIFGVKGLKYPSKEKMLSVGELESEVLL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 6197..16152
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HV215_RS25375 (HV215_25400) | 1651..1917 | + | 267 | WP_044715141 | hypothetical protein | - |
| HV215_RS25380 (HV215_25405) | 1910..2149 | + | 240 | WP_044715143 | hypothetical protein | - |
| HV215_RS25385 (HV215_25410) | 2246..2587 | + | 342 | WP_059347451 | hypothetical protein | - |
| HV215_RS25390 (HV215_25415) | 2665..2814 | + | 150 | WP_162852120 | hypothetical protein | - |
| HV215_RS25395 (HV215_25420) | 2830..3087 | + | 258 | WP_044715147 | hypothetical protein | - |
| HV215_RS25400 (HV215_25425) | 3415..3963 | + | 549 | WP_044715148 | DNA distortion polypeptide 1 | - |
| HV215_RS25405 (HV215_25430) | 3966..5126 | + | 1161 | WP_044715149 | MobP1 family relaxase | - |
| HV215_RS25410 (HV215_25435) | 5482..5973 | + | 492 | WP_044715152 | transcription termination/antitermination NusG family protein | - |
| HV215_RS25415 (HV215_25440) | 6197..6841 | + | 645 | WP_044715155 | lytic transglycosylase domain-containing protein | virB1 |
| HV215_RS25420 (HV215_25445) | 6825..7115 | + | 291 | WP_044715156 | TrbC/VirB2 family protein | virB2 |
| HV215_RS25425 (HV215_25450) | 7137..9896 | + | 2760 | WP_044715159 | VirB3 family type IV secretion system protein | virb4 |
| HV215_RS25430 (HV215_25455) | 9907..10653 | + | 747 | WP_044715162 | type IV secretion system protein | - |
| HV215_RS25435 (HV215_25460) | 10663..10920 | + | 258 | WP_044715163 | EexN family lipoprotein | - |
| HV215_RS25440 (HV215_25465) | 10932..11987 | + | 1056 | WP_044715165 | type IV secretion system protein | virB6 |
| HV215_RS25445 (HV215_25470) | 12227..12955 | + | 729 | WP_044715168 | type IV secretion system protein | virB8 |
| HV215_RS25450 (HV215_25475) | 12960..13889 | + | 930 | WP_044715170 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HV215_RS25455 (HV215_25480) | 13886..15097 | + | 1212 | WP_044715172 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| HV215_RS25460 (HV215_25485) | 15121..16152 | + | 1032 | WP_044715211 | P-type DNA transfer ATPase VirB11 | virB11 |
| HV215_RS25465 (HV215_25490) | 16155..17990 | + | 1836 | WP_044715174 | type IV secretory system conjugative DNA transfer family protein | - |
| HV215_RS25470 (HV215_25495) | 17987..18382 | + | 396 | WP_044715177 | cag pathogenicity island Cag12 family protein | - |
| HV215_RS26280 | 18387..18725 | + | 339 | WP_225622178 | hypothetical protein | - |
| HV215_RS25480 (HV215_25505) | 18794..18997 | + | 204 | WP_044715181 | hypothetical protein | - |
| HV215_RS25485 (HV215_25510) | 19003..19338 | + | 336 | WP_050886236 | hypothetical protein | - |
| HV215_RS25490 (HV215_25515) | 19335..19805 | + | 471 | WP_044715183 | thermonuclease family protein | - |
| HV215_RS25495 (HV215_25520) | 19820..20593 | + | 774 | WP_044715185 | hypothetical protein | - |
Host bacterium
| ID | 5700 | GenBank | NZ_CP055470 |
| Plasmid name | pRHBSTW-00488_5 | Incompatibility group | IncX5 |
| Plasmid size | 63151 bp | Coordinate of oriT [Strand] | 3033..3627 [-] |
| Host baterium | Citrobacter freundii strain RHBSTW-00488 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | katA, wbbO, wbbN, glf, wbbM, wzt, wzm |
| Metal resistance gene | arsR, arsD, arsA, arsB, arsC |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |