Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100589 |
| Name | oriT_pPBA  |
| Organism | Sphingobium wenxiniae |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_025133 (57279..57466 [-], 188 nt) |
| oriT length | 188 nt |
| IRs (inverted repeats) | IR1: 17..36, 37..56 (AACCGTGAAGCGCGATCCAA..TGGGATTGAGCGTAACGGTT) IR2: 115..126, 129..140 (AAAGCGGTGGCA..TGCCACCGCTCT) |
| Location of nic site | 84..86 |
| Conserved sequence flanking the nic site |
TATCCTG|C |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 188 nt
>oriT_pPBA
GGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCAATGGGATTGAGCGTAACGGTTAACATTAGCCGCCGCAAGGCTTATCCTGCCATACAGTAGATACCTACCCCACAAACAAAAAGCGGTGGCAACTGCCACCGCTCTAAATTCCACATCGCCTCGATGCTGAGTGAACGTGGACGGTAAAAGCTA
GGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCAATGGGATTGAGCGTAACGGTTAACATTAGCCGCCGCAAGGCTTATCCTGCCATACAGTAGATACCTACCCCACAAACAAAAAGCGGTGGCAACTGCCACCGCTCTAAATTCCACATCGCCTCGATGCTGAGTGAACGTGGACGGTAAAAGCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 661 | GenBank | YP_009067864 |
| Name | MobA/VirD2_pPBA |
UniProt ID | A0A059U2Z1 |
| Length | 347 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 347 a.a. Molecular weight: 38679.28 Da Isoelectric Point: 11.2122
>YP_009067864.1 endonuclease relaxase MobA/VirD2 (plasmid) [Sphingobium wenxiniae]
MSDFDSSFEAGQLAALFKPKLTSDPNRRGADMLLRSLSSRRAGQGGSTRARLARVVSRAPEVMVKVTGRP
KGKNHAAAHFDYIGRKGDVPLETRDGDILTDKEDRAELARDWGDPVYWRDNSTVAAVSMVFSMPSGTDPD
KVLSAVREVARSEIGHEWDYVLALHTDTPRPHVHVTVAARGDTGRRFNPRPQTLHHYRERFAEELRARGV
TAEATPRAARGVGRAGQSMALNRMRQRYMAGTAPAPFANQKITSAARDQLAGRSTAPDFVVRGRQAWNET
HRRYLAAAKRLEASSDPADRQLADQVREFVGAGRTPTIHERSVAAIERKRQNERSRDRDRSREGPER
MSDFDSSFEAGQLAALFKPKLTSDPNRRGADMLLRSLSSRRAGQGGSTRARLARVVSRAPEVMVKVTGRP
KGKNHAAAHFDYIGRKGDVPLETRDGDILTDKEDRAELARDWGDPVYWRDNSTVAAVSMVFSMPSGTDPD
KVLSAVREVARSEIGHEWDYVLALHTDTPRPHVHVTVAARGDTGRRFNPRPQTLHHYRERFAEELRARGV
TAEATPRAARGVGRAGQSMALNRMRQRYMAGTAPAPFANQKITSAARDQLAGRSTAPDFVVRGRQAWNET
HRRYLAAAKRLEASSDPADRQLADQVREFVGAGRTPTIHERSVAAIERKRQNERSRDRDRSREGPER
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A059U2Z1 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 23479..33452
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTC33_RS00115 | 19269..20033 | - | 765 | WP_172685733 | IS6-like element IS6100 family transposase | - |
| HTC33_RS00120 | 19999..20340 | - | 342 | WP_238839197 | hypothetical protein | - |
| HTC33_RS00125 | 20417..21595 | - | 1179 | WP_031293106 | LPD7 domain-containing protein | - |
| HTC33_RS00130 (MA31_p15) | 21585..23501 | - | 1917 | WP_021223054 | type IV secretory system conjugative DNA transfer family protein | - |
| HTC33_RS00135 (MA31_p16) | 23479..24471 | - | 993 | WP_011627746 | P-type DNA transfer ATPase VirB11 | virB11 |
| HTC33_RS00140 (MA31_p17) | 24468..25736 | - | 1269 | WP_021223055 | type IV secretion system protein VirB10 | virB10 |
| HTC33_RS00145 (MA31_p18) | 25738..26580 | - | 843 | WP_021223056 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HTC33_RS00150 (MA31_p19) | 26577..27260 | - | 684 | WP_004213217 | VirB8/TrbF family protein | virB8 |
| HTC33_RS00155 | 27270..27590 | - | 321 | WP_021223057 | hypothetical protein | - |
| HTC33_RS00160 (MA31_p20) | 27601..28617 | - | 1017 | WP_056379780 | type IV secretion system protein | virB6 |
| HTC33_RS00165 | 28658..28954 | - | 297 | WP_238839198 | hypothetical protein | - |
| HTC33_RS00170 (MA31_p21) | 28966..29679 | - | 714 | WP_021223006 | type IV secretion system protein | virB5 |
| HTC33_RS00175 (MA31_p22) | 29693..32077 | - | 2385 | WP_021223007 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HTC33_RS00180 (MA31_p23) | 32064..32408 | - | 345 | WP_006949650 | VirB3 family type IV secretion system protein | virB3 |
| HTC33_RS00185 (MA31_p24) | 32415..32756 | - | 342 | WP_004213202 | TrbC/VirB2 family protein | virB2 |
| HTC33_RS00190 (MA31_p25) | 32778..33452 | - | 675 | WP_021223008 | transglycosylase SLT domain-containing protein | virB1 |
| HTC33_RS00195 | 33467..33808 | - | 342 | WP_007016057 | hypothetical protein | - |
| HTC33_RS00200 | 33850..34158 | - | 309 | WP_004213195 | hypothetical protein | - |
| HTC33_RS00205 | 34318..34566 | + | 249 | WP_007016056 | hypothetical protein | - |
| HTC33_RS00210 | 34869..35651 | + | 783 | WP_092960426 | replication initiation protein | - |
| HTC33_RS00215 (MA31_p26) | 35763..36644 | + | 882 | WP_007016055 | toprim domain-containing protein | - |
| HTC33_RS00220 (MA31_p27) | 36638..37228 | + | 591 | WP_020819817 | thermonuclease family protein | - |
| HTC33_RS00225 | 37345..37665 | + | 321 | WP_006949645 | hypothetical protein | - |
Host bacterium
| ID | 1049 | GenBank | NC_025133 |
| Plasmid name | pPBA | Incompatibility group | _ |
| Plasmid size | 59859 bp | Coordinate of oriT [Strand] | 57279..57466 [-] |
| Host baterium | Sphingobium wenxiniae |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |