oriTDB
The information of the oriT region
oriTDB accession number 100064
Name oriT_pPDL2  insolico
Sequence Completeness core
oriT length 45 nt
oriT sequence GCTATCCCGCGCCGCTGCTGAAGAAGAAGAAAAGCGCCGCCTCTT
IR (inverted repeat)[24-34] [35-45] nt  (AAGAAGAAAAG..CGCCGCCTCTT)
Location of nic site [9-10] nt
Conserved sequence flanking the
  nic site 		TATCCCG|C
Note _
L:24-34;R:35-45;D:9-10
Visualization of oriT structure
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]
I. Information of Relaxase
ID 60
Name RepB_pPDL2 insolico
GenBank accession number YP_006965809
Family MOBF
Length 303 aa
UniProt ID K4I164
PDB ID _
Pfam Rep_3 [PF01051.20], Evalue: 2.20E-24, Aligned region: 38..257
Note relaxase
Protein sequence [Download] MNHATSPVNGGKAKVALDGDTALTLAQKGRGNPFDPANYGEIVKPGELVDIVELSPLTLA
DRRIYNLLIANAWERIGEPVIHRIPKSALKGTHQGNERIESSLLRLMGTIAIVTIRKGGK
SFKRRVQLLGPSDESLEKDGFLHYRIPEELIEILRNSEVYARLKTQVMYCFESKYALCLY
EMIERRIGLEYKQSEEFTIAELRGLLNVPEGKLERFADFNKYCLKVAQEEINKLCPFWVE
FTPIKKGRKVERVSMMWLPKTMSGRRDAQNLIDQHSIVRRAKLRGDIPEMPVLVDFSAPA
AQR
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]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 91 _ insolico
 N/A
Information of plasmid
ID 60
Plasmid name pPDL2
GenBank accession number NC_019376.1
Incompatibility group IncP1
Genome size 37317 bp
Coordinate of oriT  [Strand] 35038..35082 [+]
Drug resistance _
Heavy-metal resistance _
Virulence factor _
Xenobiotic degradation experimental organophosphate degradation(opd gene cluster)
Host bacterium [NCBI Taxonomy ID] Sphingobium fuliginis ATCC 27551 [1208342]
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]

Microbial Bioinformatics Group in MML, SJTU