oriTDB
The information of the oriT region
oriTDB accession number 100494
Name oriT_pDB1  insolico
Sequence Completeness intact
oriT length 373 nt
oriT sequence GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGT TGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCT AACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGC CATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGC GAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGC GGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAG ATGGACGAACACG
IR (inverted repeat)IR1: [64-68] [72-76] nt  (GCGCC..GGCGC)
IR2: [89-107] [110-128] nt  (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site [136-137] nt
Conserved sequence flanking the
  nic site 		CATCCTG|C
Note predicted by the oriTfinder
L:64-68;R:72-76;L:89-107;R:110-128;D:136-137
Visualization of oriT structure
Reference
 N/A
I. Information of Relaxase
ID 565
Name TraI_pDB1 insolico
GenBank accession number YP_006963148
Family MOBP
Length 746 aa
UniProt ID I3RYJ8
PDB ID _
Pfam Relaxase [PF03432.13], Evalue: 9.90E-64, Aligned region: 12..252
Note putative relaxase
Protein sequence [Download] MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTN
TRAKGDKTYHLIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIA
INKIHPTRHTMHEPYYPHRALAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVE
SLVGWIKRECLDEIKGAQSWQELHQVMRDNGMELRVRANGLVFEAGDGTMVKASTVARDL
SKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTVELYAKYKAEQQSLTTARAQA
LERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSELQAINKQFQQ
ERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEF
KAQMIRAAVDSQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPA
ADQHATGAAAVARAGDGRPAAGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRAL
SELGVVRIAGGSEVLLPRDVPRHVEQQGTQPDHALRRGISRPGTGVGQTPPGVAAADKYI
AEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALALLKRGDEVMVMPIDQATARR
LTRIAVGDAVSITAKGSIKTSKGRSR
Reference
 N/A

II. Auxiliary DNA-binding protein(s) of the relaxosome
 N/A
 N/A
Information of plasmid
ID 955
Plasmid name pDB1
GenBank accession number NC_019320.1
Incompatibility group IncP(Beta)
Genome size 65269 bp
Coordinate of oriT  [Strand] 63295..63667 [+]
Drug resistance _
Heavy-metal resistance _
Virulence factor _
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Variovorax sp. DB1 [1179817]
Reference
[1] Kim DU et al (2013) Widespread occurrence of the tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1 and p712. Plasmid. 69(3):243-8. [PMID:23376020]

Microbial Bioinformatics Group in MML, SJTU