Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101734 |
| Name | oriT_pRHB03-C11_4  |
| Organism | Escherichia fergusonii strain RHB03-C11 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_JABXVT010000004 (25621..25969 [-], 349 nt) |
| oriT length | 349 nt |
| IRs (inverted repeats) | 134..140, 154..160 (AAAATAT..ATATTTT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 349 nt
>oriT_pRHB03-C11_4
ACTGCGATGCAGGATAGGGCAAACGCCGCAAAATGACGTCTCTGACGCCATTCCGCAACGTTTGCCCGGTGACCTACAGTCGGTTCTTGTTGGAGAGTTTTATGAAATATTTGGTCAAAGAGTTTATTAACGAAAAATATACTAAGGCTGTTAATATTTTAAAGGATAACCTTAAAGAACACTATCATGTTTTTTATTGTGTGAGATTAAGTGAGATTCTTTTTCCTGCCAGTGAATATGGAACTGAACAGTTTTTTAGTGATTTTGAAAAGATAAACTCCATTTCATTACCTGTCTTAGTGTTTGATCTCAAAGAGGGTGTTCCTGTGATTGTCATTAGTCTTGATGA
ACTGCGATGCAGGATAGGGCAAACGCCGCAAAATGACGTCTCTGACGCCATTCCGCAACGTTTGCCCGGTGACCTACAGTCGGTTCTTGTTGGAGAGTTTTATGAAATATTTGGTCAAAGAGTTTATTAACGAAAAATATACTAAGGCTGTTAATATTTTAAAGGATAACCTTAAAGAACACTATCATGTTTTTTATTGTGTGAGATTAAGTGAGATTCTTTTTCCTGCCAGTGAATATGGAACTGAACAGTTTTTTAGTGATTTTGAAAAGATAAACTCCATTTCATTACCTGTCTTAGTGTTTGATCTCAAAGAGGGTGTTCCTGTGATTGTCATTAGTCTTGATGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1469 | GenBank | WP_015056831 |
| Name | mobP1_HVV61_RS23250_pRHB03-C11_4 |
UniProt ID | H9ZMK2 |
| Length | 388 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 388 a.a. Molecular weight: 44539.89 Da Isoelectric Point: 10.5067
>WP_015056831.1 MULTISPECIES: MobP1 family relaxase [Escherichia]
MGVYVDKEYRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAVTRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKDHMIDRANDPQHMMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDVGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFWSL
MGVYVDKEYRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAVTRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKDHMIDRANDPQHMMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDVGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFWSL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | H9ZMK2 |
T4CP
| ID | 1148 | GenBank | WP_000053820 |
| Name | t4cp2_HVV61_RS23315_pRHB03-C11_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: 69389.23 Da Isoelectric Point: 7.1491
>WP_000053820.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSTSQGESESEARRALVLPQELGTLDFKEEFIILKGENPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL
MSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSTSQGESESEARRALVLPQELGTLDFKEEFIILKGENPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 35113..45073
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HVV61_RS23210 (HVV61_23215) | 30429..30674 | + | 246 | WP_000356546 | hypothetical protein | - |
| HVV61_RS23215 (HVV61_23220) | 30664..30879 | + | 216 | WP_001180116 | hypothetical protein | - |
| HVV61_RS23220 (HVV61_23225) | 30972..31301 | + | 330 | WP_000866648 | hypothetical protein | - |
| HVV61_RS23225 (HVV61_23230) | 31344..31523 | + | 180 | WP_000439078 | hypothetical protein | - |
| HVV61_RS23230 (HVV61_23235) | 31545..31742 | + | 198 | WP_001675595 | hypothetical protein | - |
| HVV61_RS23235 (HVV61_23240) | 31755..32027 | + | 273 | WP_000160399 | hypothetical protein | - |
| HVV61_RS23245 (HVV61_23250) | 32353..32898 | + | 546 | WP_001426313 | DNA distortion polypeptide 1 | - |
| HVV61_RS23250 (HVV61_23255) | 32901..34067 | + | 1167 | WP_015056831 | MobP1 family relaxase | - |
| HVV61_RS23255 (HVV61_23260) | 34420..34938 | + | 519 | WP_001446885 | transcription termination/antitermination NusG family protein | - |
| HVV61_RS23260 (HVV61_23265) | 34868..35080 | + | 213 | WP_000125172 | hypothetical protein | - |
| HVV61_RS23265 (HVV61_23270) | 35113..35760 | + | 648 | WP_000953526 | lytic transglycosylase domain-containing protein | virB1 |
| HVV61_RS23270 (HVV61_23275) | 35738..36034 | + | 297 | WP_000916182 | TrbC/VirB2 family protein | virB2 |
| HVV61_RS23275 (HVV61_23280) | 36053..38806 | + | 2754 | WP_001352869 | VirB3 family type IV secretion system protein | virb4 |
| HVV61_RS23280 (HVV61_23285) | 38817..39575 | + | 759 | WP_181465247 | type IV secretion system protein | - |
| HVV61_RS23285 (HVV61_23290) | 39576..39803 | + | 228 | WP_000835349 | EexN family lipoprotein | - |
| HVV61_RS23290 (HVV61_23295) | 39813..40946 | + | 1134 | WP_000513457 | type IV secretion system protein | virB6 |
| HVV61_RS23295 (HVV61_23300) | 41191..41904 | + | 714 | WP_181465248 | type IV secretion system protein | virB8 |
| HVV61_RS23300 (HVV61_23305) | 41909..42838 | + | 930 | WP_000783379 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HVV61_RS23305 (HVV61_23310) | 42835..44040 | + | 1206 | WP_000139139 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| HVV61_RS23310 (HVV61_23315) | 44042..45073 | + | 1032 | WP_001058468 | P-type DNA transfer ATPase VirB11 | virB11 |
| HVV61_RS23315 (HVV61_23320) | 45076..46911 | + | 1836 | WP_000053820 | type IV secretory system conjugative DNA transfer family protein | - |
| HVV61_RS23320 (HVV61_23325) | 46908..47321 | + | 414 | WP_000722611 | cag pathogenicity island Cag12 family protein | - |
| HVV61_RS23325 (HVV61_23330) | 47318..47620 | + | 303 | WP_000820908 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HVV61_RS23330 (HVV61_23335) | 47721..49046 | + | 1326 | WP_000869134 | YadA C-terminal domain-containing protein | - |
| HVV61_RS23335 (HVV61_23340) | 49075..49302 | + | 228 | WP_000803715 | hypothetical protein | - |
| HVV61_RS23340 (HVV61_23345) | 49382..49891 | + | 510 | WP_000691577 | thermonuclease family protein | - |
Host bacterium
| ID | 2178 | GenBank | NZ_JABXVT010000004 |
| Plasmid name | pRHB03-C11_4 | Incompatibility group | IncX1 |
| Plasmid size | 52614 bp | Coordinate of oriT [Strand] | 25621..25969 [-] |
| Host baterium | Escherichia fergusonii strain RHB03-C11 |
Cargo genes
| Drug resistance gene | ant(3'')-Ia, aph(6)-Id, dfrA14, sul2 |
| Virulence gene | - |
| Metal resistance gene | arsH |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |