Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120498 |
| Name | oriT_pRHBSTW-00985_4  |
| Organism | Citrobacter freundii strain RHBSTW-00985 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP056211 (44700..45294 [+], 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-00985_4
TGTTAAGTACATTGTAGTTTTGATAAAATCATTAGTATCTGGCATAACTTTATCATTATCATCTTCTGTTACTTTGCTTTTAAGTAAAGCACTGGCAAGCAATTTCATGCCTTTAGCAACAGTTAAACCAGGCTCATCTGGATAAATAACCTTCAGACATTCAAGTAGATTATCATGCTGTTTTTCTTCCAGTCTGAAATTAATTTGCTTCATAAATCCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGAGTAAAATGCTAGCATTTTGCGGCGTTTGCCCTATCCTGCATCGCATTAATCTAGCACTACACTTGAATTGTGCTTCAGCGTCGATGAAAAAGCAAAACTGAAGGGCTGTCATGGCTGAAGGTTTCGCTTGTCTACGACCGGAAACACCTCAATGGCTGTAAGCTATGTGGGATAAGGTTCGCTACGCGAACGGTCTGGCAGGGGGCGCAAGCGCTGTCTTGCAGAGTATATAAAAAAGCACCTCCCGCAAACGGGAGGGCTTCGGCGATTCATGACGTGTGAAGCTATTTAGGGTCTGGTGTGACGCCTCCCATGCCCTGACGGGCATCACACAACCAG
TGTTAAGTACATTGTAGTTTTGATAAAATCATTAGTATCTGGCATAACTTTATCATTATCATCTTCTGTTACTTTGCTTTTAAGTAAAGCACTGGCAAGCAATTTCATGCCTTTAGCAACAGTTAAACCAGGCTCATCTGGATAAATAACCTTCAGACATTCAAGTAGATTATCATGCTGTTTTTCTTCCAGTCTGAAATTAATTTGCTTCATAAATCCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGAGTAAAATGCTAGCATTTTGCGGCGTTTGCCCTATCCTGCATCGCATTAATCTAGCACTACACTTGAATTGTGCTTCAGCGTCGATGAAAAAGCAAAACTGAAGGGCTGTCATGGCTGAAGGTTTCGCTTGTCTACGACCGGAAACACCTCAATGGCTGTAAGCTATGTGGGATAAGGTTCGCTACGCGAACGGTCTGGCAGGGGGCGCAAGCGCTGTCTTGCAGAGTATATAAAAAAGCACCTCCCGCAAACGGGAGGGCTTCGGCGATTCATGACGTGTGAAGCTATTTAGGGTCTGGTGTGACGCCTCCCATGCCCTGACGGGCATCACACAACCAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12907 | GenBank | WP_181624216 |
| Name | mobP1_HV344_RS25620_pRHBSTW-00985_4 |
UniProt ID | _ |
| Length | 386 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 386 a.a. Molecular weight: 44316.73 Da Isoelectric Point: 10.6126
>WP_181624216.1 MobP1 family relaxase [Citrobacter freundii]
MGVSVDKEYRVKRKSSEAGRKSAFAHKVKNGGKNYQRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGQVWKGDEIQEAKEHMVDRANDPQHVMNDKGKENKKVTQNIVFSPPVSAKVKPED
LLESARKTMQKKYPNHRFVLGYHNDKKDHPHVHVVFRIRDEDGKRTDIRKKDLREIRTGFCEELKLKGYD
VKATHRQQQGLNQSIRDAHSTAPKRQKGVYEVVDVGYDHYQHDKTKPKQHFLKLKTLNKGVEKTYWGADF
GDLTSRENVKKGDLVKLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWKLDNLGVKGIDRNPSSSKELVLN
SAAMLQKQQLQMKQFTQIKQAMLQNEQKMKIGIKLG
MGVSVDKEYRVKRKSSEAGRKSAFAHKVKNGGKNYQRNVQERINRKGASKEVVVKISGGAITRQGIRNSI
DYMSRESELPVMSESGQVWKGDEIQEAKEHMVDRANDPQHVMNDKGKENKKVTQNIVFSPPVSAKVKPED
LLESARKTMQKKYPNHRFVLGYHNDKKDHPHVHVVFRIRDEDGKRTDIRKKDLREIRTGFCEELKLKGYD
VKATHRQQQGLNQSIRDAHSTAPKRQKGVYEVVDVGYDHYQHDKTKPKQHFLKLKTLNKGVEKTYWGADF
GDLTSRENVKKGDLVKLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWKLDNLGVKGIDRNPSSSKELVLN
SAAMLQKQQLQMKQFTQIKQAMLQNEQKMKIGIKLG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 15158 | GenBank | WP_181624208 |
| Name | t4cp2_HV344_RS25560_pRHBSTW-00985_4 |
UniProt ID | _ |
| Length | 611 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 611 a.a. Molecular weight: 69253.94 Da Isoelectric Point: 6.9118
>WP_181624208.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWLFIGFVMCLFTYYAGSVAVYFFNGKTPLFIWKNFDSMLLWRLMTESNIRSDIRITAIPA
LLSGLAASVIIPVFIIWQLNKKDFSLYGDAKFASDDDLRKSKLLKWEKENDDDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREVLLQNKVFLLDPFNSKTHKFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYAPDWLNEFNLKPVFSI
GSVVDLYSNIDRENVLANREDFEGIAGLDETALFHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDISIYVGVNAEDMSLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGVEGAKTLMSAHPCRIIYAVSEEDDAKKIS
EKLGYITAKSTGSSKTSGRSTSKSNSESDAQRALVLPQELGTLEFSEEFIILKGENPVKAQKALYYLDSY
FMDRLMLVSPKLAALTSSLNKTKNIFGVKGLKYPSKEKMLSVGELESEVLL
MSLKLPDKGQWLFIGFVMCLFTYYAGSVAVYFFNGKTPLFIWKNFDSMLLWRLMTESNIRSDIRITAIPA
LLSGLAASVIIPVFIIWQLNKKDFSLYGDAKFASDDDLRKSKLLKWEKENDDDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREVLLQNKVFLLDPFNSKTHKFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYAPDWLNEFNLKPVFSI
GSVVDLYSNIDRENVLANREDFEGIAGLDETALFHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDISIYVGVNAEDMSLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGVEGAKTLMSAHPCRIIYAVSEEDDAKKIS
EKLGYITAKSTGSSKTSGRSTSKSNSESDAQRALVLPQELGTLEFSEEFIILKGENPVKAQKALYYLDSY
FMDRLMLVSPKLAALTSSLNKTKNIFGVKGLKYPSKEKMLSVGELESEVLL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 29330..42130
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HV344_RS25520 (HV344_25525) | 24450..26771 | - | 2322 | WP_181624201 | type IA DNA topoisomerase | - |
| HV344_RS25525 (HV344_25530) | 26775..28037 | - | 1263 | WP_181624202 | AAA family ATPase | - |
| HV344_RS25530 (HV344_25535) | 28119..28505 | - | 387 | WP_181624203 | hypothetical protein | - |
| HV344_RS25535 (HV344_25540) | 28516..28986 | - | 471 | WP_181624204 | thermonuclease family protein | - |
| HV344_RS25540 (HV344_25545) | 28983..29324 | - | 342 | WP_181624205 | hypothetical protein | - |
| HV344_RS25545 (HV344_25550) | 29330..29533 | - | 204 | WP_181624206 | TraM recognition domain-containing protein | virb4 |
| HV344_RS26260 | 29602..29940 | - | 339 | WP_225622178 | hypothetical protein | - |
| HV344_RS25555 (HV344_25560) | 29945..30340 | - | 396 | WP_181624207 | cag pathogenicity island Cag12 family protein | - |
| HV344_RS25560 (HV344_25565) | 30337..32172 | - | 1836 | WP_181624208 | type IV secretory system conjugative DNA transfer family protein | - |
| HV344_RS25565 (HV344_25570) | 32175..33206 | - | 1032 | WP_181624231 | P-type DNA transfer ATPase VirB11 | virB11 |
| HV344_RS25570 (HV344_25575) | 33230..34441 | - | 1212 | WP_181624209 | TrbI/VirB10 family protein | virB10 |
| HV344_RS25575 (HV344_25580) | 34438..35367 | - | 930 | WP_181624210 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HV344_RS25580 (HV344_25585) | 35372..36100 | - | 729 | WP_181624211 | virB8 family protein | virB8 |
| HV344_RS25585 (HV344_25590) | 36340..37395 | - | 1056 | WP_181624212 | type IV secretion system protein | virB6 |
| HV344_RS25590 (HV344_25595) | 37407..37664 | - | 258 | WP_181624213 | EexN family lipoprotein | - |
| HV344_RS25595 (HV344_25600) | 37674..38420 | - | 747 | WP_181624232 | type IV secretion system protein | - |
| HV344_RS25600 (HV344_25605) | 38431..41190 | - | 2760 | WP_181624214 | VirB3 family type IV secretion system protein | virb4 |
| HV344_RS25605 (HV344_25610) | 41212..41502 | - | 291 | WP_044715156 | TrbC/VirB2 family protein | virB2 |
| HV344_RS25610 (HV344_25615) | 41486..42130 | - | 645 | WP_097724924 | lytic transglycosylase domain-containing protein | virB1 |
| HV344_RS25615 (HV344_25620) | 42354..42845 | - | 492 | WP_181624215 | transcription termination/antitermination NusG family protein | - |
| HV344_RS25620 (HV344_25625) | 43201..44361 | - | 1161 | WP_181624216 | MobP1 family relaxase | - |
| HV344_RS25625 (HV344_25630) | 44364..44912 | - | 549 | WP_181624217 | DNA distortion polypeptide 1 | - |
| HV344_RS25630 (HV344_25635) | 45240..45497 | - | 258 | WP_181624218 | hypothetical protein | - |
| HV344_RS25635 (HV344_25640) | 45513..45662 | - | 150 | WP_162852120 | hypothetical protein | - |
| HV344_RS25640 (HV344_25645) | 45740..46081 | - | 342 | WP_181624219 | hypothetical protein | - |
| HV344_RS25645 (HV344_25650) | 46178..46417 | - | 240 | WP_044715143 | hypothetical protein | - |
| HV344_RS25650 (HV344_25655) | 46410..46676 | - | 267 | WP_044715141 | hypothetical protein | - |
Host bacterium
| ID | 20927 | GenBank | NZ_CP056211 |
| Plasmid name | pRHBSTW-00985_4 | Incompatibility group | IncX5 |
| Plasmid size | 48045 bp | Coordinate of oriT [Strand] | 44700..45294 [+] |
| Host baterium | Citrobacter freundii strain RHBSTW-00985 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | kpsM, kpsT, kpsS, kpsC, kpsD, kpsE |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |