Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100064 |
| Name | oriT_pPDL2  |
| Organism | Sphingobium fuliginis ATCC 27551 |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NC_019376 (35038..35082 [+], 45 nt) |
| oriT length | 45 nt |
| IRs (inverted repeats) | 24..34, 35..45 (AAGAAGAAAAG..CGCCGCCTCTT) |
| Location of nic site | 9..10 |
| Conserved sequence flanking the nic site |
TATCCCG|C |
| Note | _ |
oriT sequence
Download Length: 45 nt
>oriT_pPDL2
GCTATCCCGCGCCGCTGCTGAAGAAGAAGAAAAGCGCCGCCTCTT
GCTATCCCGCGCCGCTGCTGAAGAAGAAGAAAAGCGCCGCCTCTT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Pandeeti EV et al. (2012) Multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in Sphingobium fuliginis ATCC 27551. G3 (Bethesda). 2(12):1541-54. [PMID:23275877]
Relaxase
| ID | 60 | GenBank | YP_006965809 |
| Name | RepB_pPDL2 |
UniProt ID | K4I164 |
| Length | 303 a.a. | PDB ID | |
| Note | relaxase | ||
Relaxase protein sequence
Download Length: 303 a.a. Molecular weight: 34450.02 Da Isoelectric Point: 9.5732
>YP_006965809.1 Replication initiation protein (plasmid) [Sphingobium fuliginis ATCC 27551]
MNHATSPVNGGKAKVALDGDTALTLAQKGRGNPFDPANYGEIVKPGELVDIVELSPLTLADRRIYNLLIA
NAWERIGEPVIHRIPKSALKGTHQGNERIESSLLRLMGTIAIVTIRKGGKSFKRRVQLLGPSDESLEKDG
FLHYRIPEELIEILRNSEVYARLKTQVMYCFESKYALCLYEMIERRIGLEYKQSEEFTIAELRGLLNVPE
GKLERFADFNKYCLKVAQEEINKLCPFWVEFTPIKKGRKVERVSMMWLPKTMSGRRDAQNLIDQHSIVRR
AKLRGDIPEMPVLVDFSAPAAQR
MNHATSPVNGGKAKVALDGDTALTLAQKGRGNPFDPANYGEIVKPGELVDIVELSPLTLADRRIYNLLIA
NAWERIGEPVIHRIPKSALKGTHQGNERIESSLLRLMGTIAIVTIRKGGKSFKRRVQLLGPSDESLEKDG
FLHYRIPEELIEILRNSEVYARLKTQVMYCFESKYALCLYEMIERRIGLEYKQSEEFTIAELRGLLNVPE
GKLERFADFNKYCLKVAQEEINKLCPFWVEFTPIKKGRKVERVSMMWLPKTMSGRRDAQNLIDQHSIVRR
AKLRGDIPEMPVLVDFSAPAAQR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | K4I164 |
Reference
[1] Pandeeti EV et al. (2012) Multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in Sphingobium fuliginis ATCC 27551. G3 (Bethesda). 2(12):1541-54. [PMID:23275877]
Host bacterium
| ID | 60 | GenBank | NC_019376 |
| Plasmid name | pPDL2 | Incompatibility group | IncP1 |
| Plasmid size | 37317 bp | Coordinate of oriT [Strand] | 35038..35082 [+] |
| Host baterium | Sphingobium fuliginis ATCC 27551 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | organophosphate degradation(opd gene cluster) |
| Symbiosis gene | - |
| Anti-CRISPR | - |