===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== 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 29.0 Oct 6, 2004 including 1,990,271 entries, 612,044,833 residues This is a release of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the release 59 of the DDBJ/EMBL/GenBank entries (September 2004). 1. DAD Files DAD entries are stored in 19 separate files according to the Classification of the organisms from which the original DNA sequences are derived except for EST and TPA each of which is put into one file regardless of the classification. 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 suffix ".DAD" in the DAD standard format, and those with suffix ".DAD.fasta" in a FASTA-compatible format. 2. Recent changes 1) TPA data are provided in a separate file (ddbjtpa.DAD) from release 21. 2) Since release 21 the Locus line has been changed as follows: LOCUS BAA21794.1 263 aa PRT BCT 05-FEB-1999 Positions Contents --------- -------- 01-05 'LOCUS' 06-12 space 13-28 Locus name 29-29 space 30-40 Length of sequence, right-justified 41-41 space 42-43 aa 44-47 space 48-53 'PRT' 54-64 space 65-67 Division code 68-68 space 69-79 Date, in the form DD-MMM-YYYY (e.g., 15-MAR-1991) --------------------- 3) Some information on introns has been added since release 21. It is given as "intron_pos" in the Feature/Qualifiers. Examples: intron_pos 142:1 (2/12) means that the 2nd intron among 12 in total is located between the 1st and 2nd bases of the 142th codon (amino acid residue). intron_pos 228:0 (4/12) means that the 4th intron among 12 in total is located between the 227th and 228th codons (between the 3rd base of the 227th codon and the 1st base of the 228th codon). 4) The GSS division has been included since release 29. GSS stands for the Genome Survey Sequence, which is similar to EST, except that GSS isgenomic DNA whereas EST is cDNA. 3. Format of DAD Entries The standard format of DAD is almost the same as that of the DDBJ nucleotide sequence database except for those described below. Accession numbers of the DAD entries are written in the lines labeled as "ACCESSION." An accession number of DAD is comprised of a DDBJ accession number and an integer that begins from 1. These two numbers are combined by a hyphen (-). For example, two amino acid sequences extracted from a DDBJ entry D12345 respectively have accession numbers of D12345-1 and D12345-2. The number is useful for identifying a DAD entry. 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. The other parts of a DAD entry, including FEATURES, are almost the same as those of the corresponding DDBJ entry. 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 BAA22986.1 220 aa PRT HUM 27-OCT-1997 DEFINITION Homo sapiens RVP1 protein. ACCESSION AB000714-1 PROTEIN_ID BAA22986.1 SOURCE Homo sapiens ORGANISM Homo sapiens Eukaryotae; Metazoa; Chordata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1250) 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) 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) COMMENT FEATURES Qualifiers source /mol_type="mRNA" /organism="Homo sapiens" /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 1,990,271 total length of sequences 612,044,833 aa average length 307 aa name of longest sequence AJ277892-2 PID:CAD12456.1 length of longest sequence 34,350 aa (AJ277892-2) ====================================================== file no. of entries no. of amino acids ====================================================== ddbjbct 727,164 218,606,572 ddbjest 948 85,078 ddbjgss 6 1,476 ddbjhtc 30,450 9,976,526 ddbjhtg 1,959 1,388,568 ddbjhum 135,520 44,697,597 ddbjinv 193,955 68,178,186 ddbjmam 34,168 8,023,165 ddbjpat 40,527 12,373,420 ddbjphg 17,969 3,685,367 ddbjpln 314,439 113,103,672 ddbjpri 14,000 2,895,307 ddbjrod 87,144 30,813,112 ddbjsts 9 812 ddbjsyn 11,146 3,049,014 ddbjtpa 4,769 1,403,947 ddbjuna 791 123,186 ddbjvrl 272,060 65,778,361 ddbjvrt 103,247 27,861,467 ====================================================== total 1,990,271 612,044,833 ====================================================== DNA Data Bank of Japan Center for Information Biology and DNA Data Bank of Japan National Institute of Genetics Research Organization of Information and Systems Mishima 411-8540, Japan Phone: +81 55 981 6853 FAX: +81 55 981 6849 E-mail: ddbj@ddbj.nig.ac.jp (for general inquiry) WWW: http://www.ddbj.nig.ac.jp/ (for DDBJ WWW server)