Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100648 |
| Name | oriT_pLA2  |
| Organism | Novosphingobium pentaromativorans US6-1 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP009296 (1027..1216 [-], 190 nt) |
| oriT length | 190 nt |
| IRs (inverted repeats) | IR1: 19..38, 39..58 (AACCGTGAAGCGCGATCCGA..TAGGATTGAGCGTATCGGTT) IR2: 117..128, 131..142 (AAAGCGGTGGCA..TGCCACCGCTCT) |
| Location of nic site | 86..87 |
| Conserved sequence flanking the nic site |
TATCCTG|C |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 190 nt
>oriT_pLA2
GTGGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCGATAGGATTGAGCGTATCGGTTAACATTAGCCGCCGCAAGGCTTATCCTGCCATACAGTAGATACCTACCCCACAAACAAAAAGCGGTGGCAACTGCCACCGCTCTAAATTCCACGTCGCCTCGATGCTGAGAGAACGTGGACGGTAAAAGCTA
GTGGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCGATAGGATTGAGCGTATCGGTTAACATTAGCCGCCGCAAGGCTTATCCTGCCATACAGTAGATACCTACCCCACAAACAAAAAGCGGTGGCAACTGCCACCGCTCTAAATTCCACGTCGCCTCGATGCTGAGAGAACGTGGACGGTAAAAGCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 720 | GenBank | WP_004213271 |
| Name | PutativerelaxaseofpLA2 |
UniProt ID | G6ELI0 |
| Length | 347 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 347 a.a. Molecular weight: 38494.16 Da Isoelectric Point: 11.3910
>WP_004213271.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Sphingomonadaceae]
MSDFDSSFEAGQLAALFKPKLTSDPNRRGADMLLRSLSSRRAGQGGSTRARLARVVSRAPEVMVKVTGRP
KGKNHAAAHFDYIGRKGDVPLETRDGDILTDKEARAELARDWGDPVYWRDNSTVAAVSMVFSMPAGTDPD
KVLSAVREVARSEIGHEWDYVLALHTDTPRPHVHVTVAARGDTGQRFNPRPQTLHHYRERFAEELRARGV
TAEATPRAARGVGRAGQSMALNRMRQRYMAGTAPAPFANQKITAAARDQLAGRSTAPDFVVRGRQAWNET
QHRYLAAAKRLETSSDPADRQLADQVRQFVGAGRTPTIHERSVAAMERKRQSERSRNRDRSREGPGR
MSDFDSSFEAGQLAALFKPKLTSDPNRRGADMLLRSLSSRRAGQGGSTRARLARVVSRAPEVMVKVTGRP
KGKNHAAAHFDYIGRKGDVPLETRDGDILTDKEARAELARDWGDPVYWRDNSTVAAVSMVFSMPAGTDPD
KVLSAVREVARSEIGHEWDYVLALHTDTPRPHVHVTVAARGDTGQRFNPRPQTLHHYRERFAEELRARGV
TAEATPRAARGVGRAGQSMALNRMRQRYMAGTAPAPFANQKITAAARDQLAGRSTAPDFVVRGRQAWNET
QHRYLAAAKRLETSSDPADRQLADQVRQFVGAGRTPTIHERSVAAMERKRQSERSRNRDRSREGPGR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | G6ELI0 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 29159..39126
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| JI59_RS25225 (JI59_26165) | 25318..25548 | - | 231 | WP_004213230 | hypothetical protein | - |
| JI59_RS25230 (JI59_26170) | 25608..26057 | - | 450 | WP_004213229 | hypothetical protein | - |
| JI59_RS25235 (JI59_26175) | 26097..27275 | - | 1179 | WP_004213228 | LPD7 domain-containing protein | - |
| JI59_RS25240 (JI59_26180) | 27265..29181 | - | 1917 | WP_004213227 | type IV secretory system conjugative DNA transfer family protein | - |
| JI59_RS25245 (JI59_26185) | 29159..30151 | - | 993 | WP_004213226 | P-type DNA transfer ATPase VirB11 | virB11 |
| JI59_RS25250 (JI59_26190) | 30148..31416 | - | 1269 | WP_004213224 | type IV secretion system protein VirB10 | virB10 |
| JI59_RS25255 (JI59_26195) | 31418..32260 | - | 843 | WP_004213222 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| JI59_RS25260 (JI59_26200) | 32257..32940 | - | 684 | WP_004213217 | VirB8/TrbF family protein | virB8 |
| JI59_RS25270 (JI59_26210) | 33281..34297 | - | 1017 | WP_004213214 | type IV secretion system protein | virB6 |
| JI59_RS25275 (JI59_26215) | 34341..34646 | - | 306 | WP_006949657 | hypothetical protein | - |
| JI59_RS25280 (JI59_26220) | 34649..35362 | - | 714 | WP_006949655 | type IV secretion system protein | virB5 |
| JI59_RS25285 (JI59_26225) | 35376..37760 | - | 2385 | WP_006949654 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| JI59_RS25290 (JI59_26230) | 37747..38091 | - | 345 | WP_006949650 | VirB3 family type IV secretion system protein | virB3 |
| JI59_RS25295 (JI59_26235) | 38098..38439 | - | 342 | WP_004213202 | TrbC/VirB2 family protein | virB2 |
| JI59_RS25300 (JI59_26240) | 38461..39126 | - | 666 | WP_004213200 | lytic transglycosylase domain-containing protein | virB1 |
| JI59_RS25310 (JI59_26250) | 39524..39832 | - | 309 | WP_004213195 | hypothetical protein | - |
| JI59_RS27230 (JI59_26255) | 40088..40240 | + | 153 | WP_006949649 | hypothetical protein | - |
| JI59_RS25320 (JI59_26260) | 40543..41325 | + | 783 | WP_006949648 | hypothetical protein | - |
| JI59_RS25325 (JI59_26265) | 41443..42318 | + | 876 | WP_238532685 | toprim domain-containing protein | - |
| JI59_RS25330 (JI59_26270) | 42312..42902 | + | 591 | WP_006949646 | thermonuclease family protein | - |
| JI59_RS25335 (JI59_26275) | 43019..43339 | + | 321 | WP_006949645 | hypothetical protein | - |
Host bacterium
| ID | 1108 | GenBank | NZ_CP009296 |
| Plasmid name | pLA2 | Incompatibility group | _ |
| Plasmid size | 62341 bp | Coordinate of oriT [Strand] | 1027..1216 [-] |
| Host baterium | Novosphingobium pentaromativorans US6-1 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |