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About This Database

ORF List

Data description
Data name
ORF List
DOI
10.18908/lsdba.nbdc00471-002
Description of data contents
This is the ORF list of 234 genomes. You can access to ORF sequences and these alignments information.
Data file
File name :
genius_orf_list.zip
File URL :
File size :
15 MB
Simple search URL
https://togodb.biosciencedbc.jp/togodb/view/genius_orf_list#en
Data acquisition method

PDB, RefSeq, nr-aa, PROSITE, CATH
Data analysis method

PDB structures were assigned to nr-aa protein sequences using PSI-BLAST search. Hit regions which met a similarity threshold calculated using CATH structure information were gathered as intermediate sequences, and genome ORF sequences were assigned to these intermediate sequences by BLAST search. Thus, PDB structures were linked to genome ORF sequences via intermediate sequences.
Number of data entries

817789
Data detail
Data item Description
ORF Name

ORF Name
ORF ID

ORF ID
Superkingdom

Superkingdom of the species which contains this ORF
Species

The species which contains this ORF
Chromosome

The chromosome (Refseq ID) which contains this ORF
Alignment (PDB & Intermediate Sequence)

PDB ID and its corresponding intermediate sequence IDIt links to the alignment information.
Alignment (ORF & Intermediate Sequence)

ORF Name and its corresponding intermediate sequence IDIt links to the alignment information.
Region in PDB (3D)

The position of PDB 3D structure corresponding this ORF
Prosite Motifs (in ORF)(in PDB)

The PROSITE motif corresponding this ORF