===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== THIS DATABASE MAY BE COPIED AND REDISTRIBUTED WITHOUT PERMISSION ON THE CONDITION THAT ALL THE STATEMENTS IN THIS RELEASE NOTE ARE REPRODUCED IN EACH COPY. ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== DDBJ Amino Acid Sequence Database (DAD) Release 16.0 Jul 30, 2001 including 797,764 entries, 245,236,540 residues This is a release of DDBJ Amino Acid Sequence Database (DAD). This database was created by extracting all translated sequences from the DDBJ/EMBL/GenBank entries. This release was made from the DDBJ release 46 (July 2001). 1. DAD Files DAD entries are stored in 17 separate files according to the organisms from which amino acid sequences are derived. These 17 divisions are the same as those of the DDBJ DNA Database, except that all translated sequences from the EST sequences are put into one file of DAD. Please refer to the release note of the DDBJ release for details (filename: ddbjrel.txt). Also, there are two types of DAD files for each division. Files with suffices ".DAD" are in a standard DAD format, whereas those with suffices ".DAD.fasta" are in a FASTA-compatible format. 2. Recent changes A new division "htc" (ddbjhtc.DAD) has been added from this release. From release 11.0, "PID" label was changed to "PROTEIN_ID", and the "/protein_id" qualifier was removed from the feature part. From release 9.0, PID numbers were replaced with Protein_ID numbers. Protein_ID is expressed like AAA12345.1, where the number after a period denotes the version number. The version number is increased by one, when the original DNA sequence is updated and the protein sequence translated is changed as a result. 3. Format of DAD Entries The standard format of DAD is almost the same as that of the DDBJ nucleotide sequence database. There are, however, important differences. Some of them are described below. Accession numbers of the DAD entries are written on the lines labeled as "ACCESSION." An accession number of DAD is comprised of a DDBJ accession number and a consecutive integer that begins from 1. These two numbers are combined by a hyphen (-). For example, amino acid sequences extracted from a DDBJ entry D12345 have accession numbers D12345-1, D12345-2, etc. This number is quite useful for identifying all DAD entries. An amino acid sequence begins from the next line of "BEGIN." Up to sixty amino acids are written in one line. Following the amino acid sequence, there is a double slash (//) which means the end of the entry. LOCUS line contains locus name, length of protein, molecular type (this is always "PRT"), division name, and date of release of DNA counterpart. DEFINITION line contains species name and protein name. Other parts of DAD entries, including FEATURES, are almost the same as those of the DDBJ entries, from which DAD entries were made. 4. A Sample of DAD Entries Below is a typical sample of DAD entries. This might be useful for understanding its format and contents. ----- ----- ----- ----- sample begin ----- ----- ----- ----- LOCUS AB000714 220 aa PRT HUM 27-OCT-1997 DEFINITION Homo sapiens RVP1 protein. ACCESSION AB000714-1 PROTEIN_ID BAA22986.1 SOURCE Homo sapiens tissue_lib:lung cDNA to mRNA. ORGANISM Homo sapiens Eukaryotae; Metazoa; Chordata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 AUTHORS Katahira,J. TITLE Direct Submission JOURNAL Submitted (26-JAN-1997) to the DDBJ/EMBL/GenBank databases. Jun Katahira, Institute for Microbial Diseases, Osaka University, Department of Bacterial Toxinology; 3-1, Yamadaoka, Suita, Osaka 565, Japan (E-mail:katahira@biken.osaka-u.ac.jp, Tel:81-6-879-8285, Fax:81-6-879-8283) STANDARD full staff_review REFERENCE 2 AUTHORS Katahira,J., Sugiyama,H., Inoue,N., Horiguchi,Y., Matsuda,M. and Sugimoto,N. TITLE Clostridium perfringens enterotoxin utilizes two structurally related membrane proteins as functional receptors in vivo JOURNAL J. Biol. Chem. 272, 26652-26658 (1997) STANDARD full staff_review COMMENT FEATURES Qualifiers source /organism="Homo sapiens" /sequenced_mol="cDNA to mRNA" /tissue_lib="lung" protein /gene="hRVP1" /transl_table=1 BEGIN 1 MSMGLEITGT ALAVLGWLGT IVCCALPMWR VSAFIGSNII TSQNIWEGLW MNCVVQSTGQ 61 MQCKVYDSLL ALPQDLQAAR ALIVVAILLA AFGLLVALVG AQCTNCVQDD TAKAKITIVA 121 GVLFLLAALL TLVPVSWSAN TIIRDFYNPV VPEAQKREMG AGLYVGWAAA ALQLLGGALL 181 CCSCPPREKK YTATKVVYSA PRSTGPGASL GTGYDRKDYV // ----- ----- ----- ----- sample end ----- ----- ----- ----- 5. Statistics of DAD The following are statistics of this release of DAD. total number of entries 797,764 total length of sequences 245,236,540 aa average length 307.4 aa name of longest sequence X90568-1 PID:CAA62188.1 length of longest sequence 26,926 aa (X90568-1) ====================================================== file no. of entries no. of amino acids ====================================================== ddbjbct 229,023 68,170,156 ddbjest 947 84,797 ddbjhtc 10,465 2,601,807 ddbjhtg 2,438 669,603 ddbjhum 71,246 23,364,720 ddbjinv 92,574 34,954,969 ddbjmam 18,265 4,469,630 ddbjpat 12,181 3,836,174 ddbjphg 6,919 1,394,474 ddbjpln 125,062 47,056,205 ddbjpri 6,841 1,407,115 ddbjrod 45,947 14,816,169 ddbjsts 4 314 ddbjsyn 4,304 1,134,002 ddbjuna 246 40,723 ddbjvrl 136,025 32,444,202 ddbjvrt 35,277 8,791,480 ====================================================== total 797,764 245,236,540 ====================================================== DNA Data Bank of Japan Center for Information Biology National Institute of Genetics Mishima 411-8540, Japan Phone: +81 559 81 6853 FAX: +81 559 81 6849 E-mail: ddbj@ddbj.nig.ac.jp (for general inquiry) WWW: http://www.ddbj.nig.ac.jp (for DDBJ WWW server)