===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== 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 11.0 Apr 26, 2000 including 514,763 entries, 158,049,461 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 41 (April 2000). 1. DAD Files DAD entries are stored in 16 separate files according to the organisms from which amino acid sequences are derived. These 16 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. Important changes We made two changes in format from this release (rel 11.0). The "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 514,763 total length of sequences 158,049,461 aa average length 306.2 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 140,047 4,163,1034 ddbjest 947 84,797 ddbjhtg 66 25,937 ddbjhum 48,585 15,859,161 ddbjinv 56,548 21,102,835 ddbjmam 13,500 3,446,508 ddbjpat 5,188 1,533,339 ddbjphg 5,369 1,073,602 ddbjpln 84,135 32,515,362 ddbjpri 3,816 787,417 ddbjrod 35,915 11,304,711 ddbjsts 10 574 ddbjsyn 3,235 808,143 ddbjuna 185 33,306 ddbjvrl 93,427 21,798,579 ddbjvrt 23,790 6,044,156 ====================================================== total 514,763 158,049,461 ====================================================== 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)