DNA Data Bank of Japan DNA Database Release 21, April 1995, including 274,596 entries, 250,875,023 bases. 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. The present release contains the newest data prepared by DDBJ, NCBI/GenBank, and EBI as of April, 1995. This unified database was made possible thanks to international collaboration among the three data banks. This release was prepared by processing the data on the relational data base management system (Sybase). Because the release contains unified data, all the entries have been annotated with common feature keys. All the entries designated by the accession numbers with the prefix "D" have been collected and processed by DDBJ, and the rest have been prepared by NCBI/GenBank and EBI. For an unavoidable problem existing at present, some entries in the three databases may overlap. We apologize for this, and are trying to resolve this problem by working together with the other data banks. Note in particular that the present release includes duplicated entries over the data files. This was originally caused by the fact that GenBank no longer has a separate file for organella, and data belonging to this category were allocated to the other files according to the "host" species. For example, a human mitochondrial DNA sequence now belongs to the primate file in the GenBank database. We, however, still maintain the organella file in this release. To revive the organella file in the GenBank database and incorporate it in this release was nevertheless quite cumbersome and time-consuming, and did not allow us to get complete results. Namely, the pertinent files other than the organella file still include the data from organella. Thus please be careful when you want to get some results only for nuclear sequences. This release includes EST(Expressed Sequence Tag)/TSF(Transcribed Sequence Fragment) data. Though we created a separate file for this category, we could not completely separate it from the other files, and could not but let the EST/TSF file fall in the same situation as in the organella file. That is, there are duplicated entries similar to those of organella data. Thus again be careful. As you may realize, the human sequence at present occupies more than half of the primate division and keeps rapidly expanding. We now think that it is better to separate them from the rest of the primate division. Thus from the next release (the 22nd release) we will set up a new division solely for human sequences. The other primate sequences will be put in the primate division. The present release also contains a file for patent sequences and related information. The patent data are those which the European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office collected and processed. The accession numbers of the patent data collected by the Japanese Patent Office start with the prefix "E" . We would warn you that unauthorized use of the patent data may cause legal issues for which we have no responsibility. This release does not include amino acid sequence data, because the genetic code system is known to be no longer uniform among species and organella, and we are not yet prepared for this. Published by: K. Ikeo, T. Imanishi, K. Goto, M. Horie, M. Iwase, M. Saito, Y. Sato, Y. Hasegawa, Y. Hattori, M. Shimoyama, A. Hasegawa, A. Suzuki, H. Tsutsui, R. Suzuki, R. Uchida, Y. Shidahara, M. Gojobori, Y. Yamaguchi, K. Nomura, S. Nagira, Y. Daito, A. Watanabe, Y. Ueda, T. Kawamoto, M. Hirashima, Y. Yamamoto, N. Shirakabe, K. Okuda, K. Ichikawa, K. Hatakeyama, N. Nakaya, T. Ito, T. Sakamaki, T. Tamura, N. Saitou, T. Gojobori, and Y. Tateno DNA Data Bank of Japan National Institute of Genetics Mishima 411, Japan Phone: +81 559 81 6853 FAX: +81 559 81 6849 E-mail: ddbj@ddbj.nig.ac.jp (for general inquiry) ddbjsub@ddbj.nig.ac.jp (for data submissions) ddbjupdt@ddbj.nig.ac.jp (for updates and notification of publication) Acknowledgement: We are grateful to NCBI, EBI, and NCGR for permitting us to include their data in the present release. We also thank the Japanese Patent Office and Japan Patent Information Organization for kindly allowing us to distribute the patent data they collected and processed. DDBJ Database Release History Release Date Entries Bases comments -------------------------------------------------------------------- 21 04/95 274,596 250,875,023 GenBank and EMBL included 20 01/95 239,689 231,299,557 GenBank and EMBL included 19 10/94 204,332 205,274,131 GenBank and EMBL included 18 07/94 185,230 192,473,021 GenBank and EMBL included 17 04/94 169,957 179,942,209 GenBank and EMBL included 16 01/94 154,626 165,017,628 GenBank and EMBL included 15 10/93 131,649 147,224,690 GenBank and EMBL included 14 07/93 120,350 138,686,333 GenBank and EMBL included 13 04/93 112,067 129,784,445 GenBank and EMBL included 12 01/93 97,683 120,815,244 GenBank and EMBL included 11 07/92 65,693 84,839,075 GenBank and EMBL included 10 01/92 59,317 77,805,556 GenBank and EMBL included 9 07/91 1,130 2,002,124 DDBJ only 8 01/91 879 1,573,442 DDBJ only 7 07/90 681 1,154,211 DDBJ only 6 01/90 496 841,236 DDBJ only 5 07/89 395 679,378 DDBJ only 4 01/89 302 535,985 DDBJ only 3 07/88 230 345,850 DDBJ only 2 01/88 142 199,392 DDBJ only 1 07/87 66 108,970 DDBJ only -------------------------------------------------------------------- Statistics of Nucleotide Sequence Data by Divisions --------------------------------------------------------------------- Division No. Entries No. Nucleotides --------------------------------------------------------------------- Primates 38,563 37,598,826 Rodents 24,728 27,292,972 Mammals 6,919 7,481,129 Other vertebrates 8,374 9,050,584 Invertebrates 21,018 29,313,218 Plants 32,480 42,579,726 Organella 10,937 13,784,877 Bacteria 19,500 35,169,827 RNAs 4,864 2,506,517 Viruses 21,319 24,681,766 Phages 1,055 1,563,756 Synthetic DNA 9,814 5,013,260 EST 86,103 27,448,123 STS 9,195 2,885,759 Unannotated sequences 3,601 926,009 Patents* 5,719 2,989,699 --------------------------------------------------------------------- Total 304,189 270,286,048 --------------------------------------------------------------------- Total(without duplication)** 274,596 250,875,023 --------------------------------------------------------------------- *: Patented sequence data processed by JAPIO (E numbers) are not included. **: DDBJ release include some duplicated entries mainly for organella and EST. These duplications were eliminated for numbers on this row. This release covers 16 categories of organisms and others as follows: ------------------------------------------------------------------------------ ddbjbct.*** Category for bacteria ddbjest.*** Category for EST (expressed sequence tag) ddbjinv.*** Category for invertebrates ddbjmam.*** Category for mammals ddbjorg.*** Category for organella ddbjpat.*** Category for patents ddbjphg.*** Category for phages ddbjpln.*** Category for plants ddbjpri.*** Category for primates ddbjrna.*** Category for RNAs ddbjrod.*** Category for rodents ddbjsts.*** Category for STS (sequence tagged site) ddbjsyn.*** Category for synthetic DNAs ddbjuna.*** Category for unannotated sequences ddbjvrl.*** Category for viruses ddbjvrt.*** Category for vertebrates other than mammals, primates, and rodents ------------------------------------------------------------------------------ Each category then has the following nine files. Note that all the files except for ddbj***.seq and ddbj***.sdr may include more than 80 characters in one line. If this is the case, the line is folded at every 81th column in the file on the distribution tape with the fixed record size of 80 bytes. ------------------------------------------------------------------------------ ddbj***.seq List of an entry in DDBJ format, see Table 1. ddbj***.acc List of the accession numbers, see Table 2 . ddbj***.aut List of the authors, see Table 3. ddbj***.dir List of the short directory in DDBJ style, see Table 4. ddbj***.idx List of indices, see Table 5. ddbj***.jou List of the journals, see Table 6. ddbj***.key List of the key words, see Table 7. ddbj***.org List of the species names, see Table 8. ddbj***.sdr List of the short directory in GenBank style, see Table 9. ------------------------------------------------------------------------------ Table 1. Part of the contents in the file 'ddbjbct.seq'. This shows all pieces of information on one entry in DDBJ format. ------------------------------------------------------------------------------ LOCUS ABCAARAA 1624 bp ds-DNA BCT 15-SEP-1990 DEFINITION A.aceti acetic acid resistance protein (aarA) gene, complete cds. ACCESSION M34830 KEYWORDS acetic acid resistance protein. SOURCE A.aceti (strain 10-8) DNA, clone pAR1611. ORGANISM Acetobacter aceti Prokaryota; Bacteria; Gracilicutes; Scotobacteria; Aerobic rods and cocci; Azotobacteraceae. REFERENCE 1 (bases 1 to 1624) AUTHORS Fukaya,M., Takemura,H., Okumura,H., Kawamura,Y., Horinouchi,S. and Beppu,T. TITLE Cloning of genes responsible for acetic acid resistance in acetobacter aceti JOURNAL J. Bacteriol. 172, 2096-2104 (1990) STANDARD simple staff_entry FEATURES Location/Qualifiers RBS 171..176 /note="ribosome binding site (put.)" CDS 185..1495 /note="acetic acid resistance protein (aarA)" /codon_start=1 misc_signal 1508..1545 /note="transcription termination signal" BASE COUNT 400 a 446 c 404 g 374 t ORIGIN 1 gcatgcattt gcacacattc gcgcgaccct aagcccaaaa aactgtggtt ttccaagcat 61 actcctttcc gataacgctt cgtttatcgc tggcaacctt ccggtttcct tttgaatgag 121 tgacaaagtg tgacgagcag gccgcagcag cgaccgtggc ccaaccatgc agaaggaaac 181 actaatgagc gcgtcgcaga aagaaggtaa gctatctacc gctaccattt cggttgatgg 241 aaaatccgcc gaaatgcctg tgctttcagg cactctggga ccggatgtta tcgacatccg 301 caaacttccg gcgcaactgg gcgttttcac gtttgaccca ggttacgggg aaacagcggc 361 ctgcaacagc aaaatcacct ttattgatgg tgataaaggc gttctgctgc accgtggtta 421 ccctattgcg cagctggacg aaaatgcttc ctacgaagaa gttatttatc tgcttttgaa 481 tggcgaactg cccaacaagg tgcagtacga caccttcacc aacaccctta caaaccatac 541 gctgctgcac gagcagatcc gtaacttctt taacggcttc cggcgtgatg cccacccaat 601 ggccattctg tgtggtacgg ttggggcttt gtctgccttc tacccagatg ccaacgatat 661 tgccattccc gccaatcggg atctggccgc catgcggctg attgccaaaa tcccaaccat 721 tgcggcatgg gcttacaaat acacgcaggg tgaagccttt atctacccgc ggaatgatct 781 gaactacgca gaaaacttcc tgtccatgat gttcgcgcgc atgtccgaac cttacaaggt 841 caaccctgtt ctggcccgcg ccatgaaccg gattctgatt ctgcatgccg atcatgagca 901 gaatgcctct acctccaccg tacgtctggc tggttctaca ggggccaatc cgtttgcctg 961 tattgctgcg ggcattgccg ctctgtgggg acctgcacat ggtggcgcaa acgaagctgt 1021 gctgaaaatg ctggcccgta ttggcaagaa agaaaatatt cctgccttta tcgcacaggt 1081 gaaggacaag aacagcggcg taaagctgat gggctttggc caccgcgttt acaagaactt 1141 cgacccacgt gcgaagatca tgcagcagac ctgccacgaa gtgctgacag aacttggcat 1201 taaggatgat ccgctgctgg atctggcggt tgagctggaa aagattgctc tgagcgatga 1261 ttacttcgtg cagcgcaaac tttacccgaa tgtggatttc tactctggca tcattctcaa 1321 ggccatgggc atccccacca gtatgtttac tgtgctgttt gccgtagccc gcaccaccgg 1381 ctgggtgagc cagtggaagg aaatgattga agaaccgggc cagcgtatca gccgccctcg 1441 ccagctttat attggcgcac cgcagcgtga ctatgtgccg cttgccaaac gctaaaacag 1501 actaacccaa aaagccgact tcccgtaagg aaagtcggct ttttgtttgc acgctgtttc 1561 caaaaaaata gggcggcaga gcgaataaac gctacctagc cttcaggcat aaaaaaacgc 1621 atgc // ------------------------------------------------------------------------------ Table 2. Part of the contents in the file 'ddbjbct.acc'. The first column refers to the secondary accession number, second column to the locus name, and third to the primary accession number. The primary number may be the same as the secondary number. They are arranged in the ascending order of the secondary accession numbers. ------------------------------------------------------------------------------ D00001 -> ECOPBPAA X04516 D00002 -> ECOPYRH X04469 D00006 -> PNS981TET D00006 D00020 -> COLE2LYS D00020 D00021 -> COLE31YS D00021 D00038 -> BRLAM330 D00038 D00066 -> BAC139AC D00066 D00067 -> ECONANA M20207 D00069 -> ECOUVRD2 D00069 D00087 -> BACXYNAA D00087 ------------------------------------------------------------------------------ Table 3. Part of the contents in the file 'ddbjbct.aut'. For each author name given on the left to the arrow, the corresponding locus name and primary accession number are respectively listed on the right. They are arranged in the alphabetical order of the author names. ------------------------------------------------------------------------------ Aan,F. -> STYCRR X05210 Aan,F. -> STYENZI M76176 Aaronson,W. -> ECOKPSD M64977 Aaronson,W. -> ECONEUA J05023 Abad-Lapuebla,M.A. -> VIBTDHI D90238 Abdel-Mawgood,A.L. -> CYAPSBHA X16394 Abdel-Meguid,S.S. -> TRNGDRECM J01843 Abdelal,A. -> STYCARA M36540 Abdelal,A. -> STYCARAB X13200 Abdelal,A.H. -> PSENOSA M60717 ------------------------------------------------------------------------------ Table 4. Part of the short directory in DDBJ style in the file 'ddbjbct.dir'. For each locus name given in the first column, the corresponding primary accession number, molecular type, number of nucleotide pairs, and description for the locus are respectively listed. They are arranged in the alphabetical order of the locus names. ------------------------------------------------------------------------------ ABCAARAA M34830 ds-DNA 1624 A.aceti acetic acid resistance protein (aarA) gene, complete cds. ABCADHCC D00635 ds-DNA 4230 A. polyoxogenes alcohol dehydrogenase (EC 1.1.99.8) and cytochrome c genes. ABCALDH D00521 ds-DNA 2683 A.polyoxogenes membrane-bound aldehyde dehydrogenase gene, complete cds and flanks. ABCBCSAA M37202 ds-DNA 9540 A.xylinum bcs B, bcs C and bcs D genes, complete cds and bcs A gene, partial cds. ABCCELA M76548 ds-DNA 1165 Acetobacter xylinum UDP pyrophosphorylase (celA) gene, complete cds. ABCCELSYN X54676 ds-DNA 5363 A. xylinum gene for cellulose biosynthesis ABCIS1380 D10043 ds-DNA 1665 A.pasteurianus insertion sequence IS1380. ACAADH1 D90004 ds-DNA 2467 Acetobacter aceti(K6033) alcohol dehydrogenase subunit gene(adh1). ACCAAC2 M62833 ds-DNA 1123 Acinetobacter baumannii aminoglycoside acetyltr ansferase (aac2) gene, complete cds. ACCACEAA M62822 ds-DNA 1874 A.baumannii chloramphenicol acetyltransferase (cat) gene, complete cds. ------------------------------------------------------------------------------ Table 5. Part of the contents in the file 'ddbjbct.idx'. The first column refers to the locus name, second column to the starting site of the locus in byte, and third to its ending site in byte. They are arranged in the alphabetical order of the locus names. ------------------------------------------------------------------------------ %***************************** #ABCAARAA 0 3211 #ABCADHCC 3212 10608 #ABCALDH 10609 15864 #ABCBCSAA 15865 29583 #ABCCELA 29584 32289 #ABCCELSYN 32290 40960 #ABCIS1380 40961 44711 #ACAADH1 44712 49357 #ACCAAC2 49358 52395 ------------------------------------------------------------------------------ Table 6. Part of the contents in the file 'ddbjbct.jou'. This gives information on the journal in which sequence data were published. ------------------------------------------------------------------------------ (in) Chaloupka,J. and Krumphanzl,V. (Eds.); Extracellular Enzymes of Microorganisms: 129-137, Plenum Press, New York (1987) -> BACAMYABS M57457 (in) Ganesan,A.T., Chang,S. and Hoch,J.A. (Eds.); Molecular Cloning and Gene Regulation in Bacilli: 3-10, Academic Press, New York (1982) -> BACRG16S M55011 (in) Ganesan,A.T., Chang,S. and Hoch,J.A. (Eds.); Molecular Cloning and Gene Regulation in Bacilli: 3-10, Academic Press, New York (1982) -> BACRG16SA M55006 (in) Ganesan,A.T., Chang,S. and Hoch,J.A. (Eds.); Molecular Cloning and Gene Regulation in Bacilli: 3-10, Academic Press, New York (1982) -> BACRG16SB M55008 (in) Hoch,J.A. and Setlow,P. (Eds.); Molecular Biology of Microbial Differentiation: 85-94, American Society for Microbiology, Washington, DC (1985) -> BACSPOII M57606 (in) Holmgren,A. (Ed.); Thioredoxin and Glutaredoxin Systems: Structure and Function: 11-19, Unknown name, Unknown city (1986) -> ECOTRXA1 M54881 (in) Kjeldgaard,N.C. and Maaloe,O. (Eds.); Control of ribosome synthesis: 138- 143, Academic Press, New York (1976) -> ECOLAC J01636 (in) Losick,R. and Chamberlin,M. (Eds.); RNA polymerase: 455-472, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1976) -> ECOTGY1 K01197 (in) Sikes,C.S. and Wheeler,A.P. (Eds.); Surface reactive peptides and polymers. Discovery and commercialization.: 186-200, American Chemical Society, Washington, D.C. (1991) -> ECOTGP J01714 (in) Sund,H. and Blauer,G. (Eds.); Protein-Ligand Interactions: 193-207, Walter de Gruyter, New York (1975) -> ECOLAC J01636 (in) Wu,R. and Grossman,L. (Eds.); Methods in Enzymology, Recombinant DNA, part E: In press, Academic Press, New York, N.Y. (1986) -> PLMCG M11320 Acta Microbiol. Pol. 35, 175-190 (1986) -> ECOTGG1 M54893 Actinomycetologica 5, 14-17 (1991) -> STMARGG D00799 Adv. Biophys. 21, 115-133 (1986) -> R10REP M26840 Adv. Biophys. 21, 175-192 (1986) -> ECONUSAA M26839 Adv. Enzyme Regul. 21, 225-237 (1983) -> ECOPURFA M26893 Adv. Exp. Med. Biol. 195, 239-246 (1986) -> ECOAPT M14040 Agric. Biol. Chem. 50, 2155-2158 (1986) -> ECONANA M20207 Agric. Biol. Chem. 50, 2771-2778 (1986) -> BRLAM330 D00038 Agric. Biol. Chem. 51, 2019-2022 (1987) -> BACCGT D00129 Agric. Biol. Chem. 51, 2641-2648 (1987) -> STRSAGP D00219 Agric. Biol. Chem. 51, 2807-2809 (1987) -> BACPGECR M35503 Agric. Biol. Chem. 51, 3133-3135 (1987) -> BACXYLAP D00312 Agric. Biol. Chem. 51, 455-463 (1987) -> BACHDCRY D00117 Agric. Biol. Chem. 51, 953-955 (1987) -> BACXYNAA D00087 Agric. Biol. Chem. 52, 1565-1573 (1988) -> BACIP135 D00348 Agric. Biol. Chem. 52, 1785-1789 (1988) -> BACTMR D00343 Agric. Biol. Chem. 52, 2243-2246 (1988) -> PSEGI D00342 Agric. Biol. Chem. 52, 399-406 (1988) -> BACAMYEB M35517 Agric. Biol. Chem. 52, 479-487 (1988) -> ECAPALI D00217 ------------------------------------------------------------------------------ Table 7. Part of the contents in the file 'ddbjbct.key'. For the locus and accession number respectively given on the right to the arrow, the corresponding key words are listed on the left. ------------------------------------------------------------------------------ A.aceti acetic acid resistance protein (aarA) gene, complete cds. -> ABCAARAA M34830 acetic acid resistance protein. -> ABCAARAA M34830 Cloning of genes responsible for acetic acid resistance in acetobacter aceti -> ABCAARAA M34830 A. polyoxogenes alcohol dehydrogenase (EC 1.1.99.8) and cytochrome c genes. -> ABCADHCC D00635 alcohol dehydrogenase; cytochrome c. -> ABCADHCC D00635 Cloning and sequencing of the gene cluster encoding two subunits of membrane- bound alcohol dehydrogenase from Acetobacter polyoxogenes -> ABCADHCC D00635 These data kindly submitted in computer readable form by: Toshimi Tamaki Nakano Central Biochemical Institute 2-6 Nakamura-cho Handa-shi, Aichi-ken 475 Japan Phone: 0569-21-3331 Fax: 0569-23-8486 -> ABCADHCC D00635 A.polyoxogenes membrane-bound aldehyde dehydrogenase gene, complete cds and flanks. -> ABCALDH D00521 aldehyde dehydrogenase gene; ethanol oxidation; membrane-bound enzyme. -> ABCALDH D00521 Nucleotide sequence of the membrane-bound aldehyde dehydrogenase gene from Acetobacter polyoxogenes -> ABCALDH D00521 ------------------------------------------------------------------------------ Table 8. Part of the contents in the file 'ddbjbct.org'. For the locus and accession number respectively given on the right to the arrow, the corresponding taxonomic names are listed on the left. They are arranged in the alphabetical order of the species names. ------------------------------------------------------------------------------ A. nidulans 6301 DNA. Anacystis nidulans Prokaryota; Bacteria; Gracilicutes; Oxyphotobacteria; Cyanobacteria. -> ANIRUBPS X00019 A. nidulans DNA, clone pAN4. Anacystis nidulans Prokaryota; Bacteria; Gracilicutes; Oxyphotobacteria; Cyanobacteria. -> ANIRGGX X00343 A. nidulans DNA. Anacystis nidulans Prokaryota; Bacteria; Gracilicutes; Oxyphotobacteria; Cyanobacteria. -> ANIRGG X00512 A. polyoxogenes genomic DNA. Acetobacter polyoxogenes Prokaryota; Bacteria; Gracilicutes; Scotobacteria; Aerobic rods and cocci; Azotobacteraceae. -> ABCADHCC D00635 A. quadruplicatum (strain PR-6) DNA, clone pAQPR1. Agmenellum quadruplicatum Prokaryota; Bacteria; Gracilicutes; Oxyphotobacteria; Cyanobacteria. -> AQUPCAB K02660 A. quadruplicatum (strain PR6) DNA. Agmenellum quadruplicatum Prokaryota; Bacteria; Gracilicutes; Oxyphotobacteria; Cyanobacteria. -> AQUCPCAB K02659 A. vinelandii DNA. Azotobacter vinelandii Prokaryota; Bacteria; Gracilicutes; Scotobacteria; Aerobic rods and cocci; Azotobacteraceae. -> AVINIFUSV M17349 A.aceti (strain 10-8) DNA, clone pAR1611. Acetobacter aceti Prokaryota; Bacteria; Gracilicutes; Scotobacteria; Aerobic rods and cocci; Azotobacteraceae. -> ABCAARAA M34830 A.actinomycetemcomitans (strain JP2) DNA, clone lambda-OP8. Actinobacillus actinomycetemcomitans Prokaryota; Bacteria; Gracilicutes; Scotobacteria; Facultatively anaerobic rods; Pasteurellaceae. -> ACNLKTXN M27399 A.anitratum DNA, clone pLJD1. Acinetobacter anitratum Prokaryota; Bacteria; Gracilicutes; Scotobacteria; Neisseriaceae. -> ACCCITSYN M33037 ------------------------------------------------------------------------------ Table 9. Part of the short directory file in GenBank style in the file 'ddbjbct.sdr'. The short directory file contains brief descriptions of all of the sequence entries contained in the GenBank style. ------------------------------------------------------------------------------ ABCAARAA A.aceti acetic acid resistance protein (aarA) gene, complete 1624bp ABCADHCC A. polyoxogenes alcohol dehydrogenase (EC 1.1.99.8) and 4230bp ABCALDH A.polyoxogenes membrane-bound aldehyde dehydrogenase gene, 2683bp ABCBCSABCD A.xylinum bcs A, B, C and D genes, complete cds's. 9540bp ABCCELA Acetobacter xylinum UDP pyrophosphorylase (celA) gene, 1165bp ABCCELSYN A. xylinum gene for cellulose biosynthesis 5363bp ABCIS1380 A.pasteurianus insertion sequence IS1380. 1665bp ACAADH1 Acetobacter aceti(K6033) alcohol dehydrogenase subunit 2467bp ACCAAC2 Acinetobacter baumannii aminoglycoside acetyltransferase 1123bp ACCACEAA A.baumannii chloramphenicol acetyltransferase (cat) gene, 1874bp ACCAPHA6 Acinetobacter baumannii aphA-6 gene. 1170bp ACCBENABCA A.calcoaceticus BenA, BenB, BenC, BenD, and BenE proteins 15922bp ACCCAT Acinetobacter calcoaceticus cat operon. 15922bp ACCCATAM A.calcoaceticus catA and catM genes, encoding catechol 1, 5537bp ACCCHMO Acinetobacter sp. cyclohexanone monooxygenase gene, complete 2128bp ACCCITSYN A.anitratum citrate synthase gene, complete cds. 1895bp ------------------------------------------------------------------------------ In addition to the 9 tables the five following index files are included in this release. These files were prepared irrespective of the 14 categories of taxonomic divisions. Accession number index file Keyword phrase index file Author name index file Journal citation index file Gene name index file A brief description is given for each file in the following. Table 10. Part of the accession number index file in the 'ddbjacc.idx'. The following excerpt from the accession number index file illustrates the format of the index. Note that as mentioned above there are such a case where an accession number for a taxonomic category is the same as that for EST or ORG; for example, PRI D12345 and EST D12345 under the same accession number D12345. ------------------------------------------------------------------------------ M33790 SHFINVEA BCT M33790 M33791 BACORF2 BCT M33791 M33792 FTRCPRBCLC ORG X55829 FTRCPRBCLC PLN X55829 M33793 FTRCPPRBCL ORG X55830 FTRCPPRBCL PLN X55830 M33794 ATPCPARRBC ORG X55831 ATPCPARRBC PLN X55831 ATPCPRBCLB ORG X15925 ATPCPRBCLB PLN X15925 M33796 NRACPNTRBC ORG X55827 NRACPNTRBC PLN X55827 M33797 NRACPRBCL ORG X55828 NRACPRBCL PLN X55828 M33798 ACCPCACGH BCT M33798 M33799 PSETRPEGDC BCT M33799 ------------------------------------------------------------------------------ Table 11. Part of the keyword phrase index file in the 'ddbjkey.idx'. Keyword phrases consist of names for gene products and other characteristics of sequence entries. ------------------------------------------------------------------------------ A CHANNEL DROCHA INV M17155 A COMPONENT SQLCVEA VRL M38183 A LOCUS GORGOGOA3 PRI X54375 GORGOGOA4 PRI X54376 A LOCUS ALLELE GORA0101 PRI X60258 GORA0201 PRI X60259 GORA0401 PRI X60257 GORA0501 PRI X60256 A MULTI-GENE FAMILY RICGLUTE PLN D00584 A PROTEIN MS2AAR PHG M25187 ST1APCS PHG M25396 A SEQUENCE HS5TOA30 VRL D00148 HS5TOA31 VRL D00147 ------------------------------------------------------------------------------ Table 12. Part of the author name index file in 'ddbjaut.idx'. The author name index file lists all of the author names that appear in the citations. ------------------------------------------------------------------------------ ABE,A. HUMMHDRBWE PRI M27509 HUMMHDRBWF PRI M27510 HUMMHDRBWG PRI M27511 YSCGAL11A PLN M22481 ABE,C. S85445 BCT S85445 ABE,E. M23442 UNA M23442 ABE,H. CHKADF VRT M55660 CHKCOF VRT M55659 ABE,K. CHPCLAC PRI D11383 CHPIMRF PRI D11384 CUGCUR09 PLN X64110 CUGCUR37 PLN X64111 HPCCEXPA VRL M55970 HPCCPEP1 VRL D10687 HPCCPEP2 VRL D10688 HPCHABC82 VRL X51587 HPCNS2APA VRL M55972 HPCNS2PA VRL M55971 HPCNS2PB VRL M55973 HPCNS5PA VRL M55974 MUSKE2 ROD M65255 MUSKE2A ROD M65256 MZECYS PLN D10622 RICCPI PLN J03469 RICGLUTE PLN D00584 RICLNOCI PLN J05595 RICOCS PLN M29259 RICORYII PLN X57658 RICOZA PLN D90406 RICOZB PLN D90407 RICOZC PLN D90408 S54524 PLN S54524 S54526 PLN S54526 S54530 PLN S54530 S73960 ROD S73960 ------------------------------------------------------------------------------ Table 13. Part of the journal citation index file in 'ddbjjou.idx'. The journal citation index file lists all of the citations that appear in the references. ------------------------------------------------------------------------------ ACTA BIOCHIM. BIOPHYS. SIN. 23, 246-253 (1992) HUMPLASINS PRI M98056 ACTA BIOCHIM. POL. 24, 301-318 (1977) LUPTRFJ RNA K00345 LUPTRFN RNA K00346 ACTA BIOCHIM. POL. 26, 369-381 (1979) BLYTRNPHE PLN X02683 ACTA BIOCHIM. POL. 29, 143-149 (1982) EMEMTA ORG M32572 EMEMTA PLN M32572 EMEMTB ORG M32573 EMEMTB PLN M32573 EMEMTC ORG M32574 EMEMTC PLN M32574 EMEMTD ORG M32575 EMEMTD PLN M32575 EMEMTE ORG M32576 EMEMTE PLN M32576 ACTA BIOCHIM. POL. 34, 21-27 (1987) LUPNOSP PLN M32571 ------------------------------------------------------------------------------ Table 14. Part of the gene name index file in 'ddbjgen.idx'. This file lists all the gene names that appear in the feature table. ------------------------------------------------------------------------------ AACC8 STMAACC8 BCT M55426 AACC9 MPUAACC9 BCT M55427 AACT HUMA1ACM PRI K01500 HUMA1ACMA PRI X00947 HUMA1ACMB PRI M18035 HUMAACT1 PRI M18906 HUMAACT2 PRI M22533 HUMAACTA PRI J05176 AAD INTINTORF BCT L06418 LMOMO229D BCT X17478 AAD A1 ENTAAC3VI BCT M88012 AAD9 ENEAAD9A BCT M69221 AADA LMOMO229A BCT X17479 S52249 BCT S52249 SYNAADA SYN M60473 TRNTAAB BCT M55547 TRNTN21CAS BCT M86913 ------------------------------------------------------------------------------ The files in this release are arranged in the following order with non-labeled format. Release note FILE.001 ddbjrel.txt 768 records Category for bacteria, 19500 entries, 35169827 bases FILE.002 ddbjbct.acc 21715 records FILE.003 ddbjbct.aut 75841 records FILE.004 ddbjbct.dir 19500 records FILE.005 ddbjbct.idx 19501 records FILE.006 ddbjbct.jou 31575 records FILE.007 ddbjbct.key 89233 records FILE.008 ddbjbct.org 19500 records FILE.009 ddbjbct.sdr 19500 records FILE.010 ddbjbct.seq 1368750 records Category for EST (expressed sequence tag), 86103 entries, 27448123 bases FILE.011 ddbjest.acc 86134 records FILE.012 ddbjest.aut 283703 records FILE.013 ddbjest.dir 86103 records FILE.014 ddbjest.idx 86104 records FILE.015 ddbjest.jou 108903 records FILE.016 ddbjest.key 353492 records FILE.017 ddbjest.org 86103 records FILE.018 ddbjest.sdr 86103 records FILE.019 ddbjest.seq 3801498 records Category for invertebrates, 21018 entries, 29313218 bases FILE.020 ddbjinv.acc 22594 records FILE.021 ddbjinv.aut 85970 records FILE.022 ddbjinv.dir 21018 records FILE.023 ddbjinv.idx 21019 records FILE.024 ddbjinv.jou 28271 records FILE.025 ddbjinv.key 90825 records FILE.026 ddbjinv.org 21018 records FILE.027 ddbjinv.sdr 21018 records FILE.028 ddbjinv.seq 1306660 records Category for mammals, 6919 entries, 7481129 bases FILE.029 ddbjmam.acc 7702 records FILE.030 ddbjmam.aut 26953 records FILE.031 ddbjmam.dir 6919 records FILE.032 ddbjmam.idx 6920 records FILE.033 ddbjmam.jou 10128 records FILE.034 ddbjmam.key 30697 records FILE.035 ddbjmam.org 6919 records FILE.036 ddbjmam.sdr 6919 records FILE.037 ddbjmam.seq 380374 records Category for organella, 10937 entries, 13784877 bases FILE.038 ddbjorg.acc 11604 records FILE.039 ddbjorg.aut 37747 records FILE.040 ddbjorg.dir 10937 records FILE.041 ddbjorg.idx 10938 records FILE.042 ddbjorg.jou 17558 records FILE.043 ddbjorg.key 49995 records FILE.044 ddbjorg.org 10937 records FILE.045 ddbjorg.sdr 10937 records FILE.046 ddbjorg.seq 649811 records Category for patents, 5719 entries, 2989699 bases FILE.047 ddbjpat.acc 5719 records FILE.048 ddbjpat.aut 17221 records FILE.049 ddbjpat.dir 5719 records FILE.050 ddbjpat.idx 5720 records FILE.051 ddbjpat.jou 5719 records FILE.052 ddbjpat.key 22640 records FILE.053 ddbjpat.org 5719 records FILE.054 ddbjpat.sdr 5719 records FILE.055 ddbjpat.seq 166676 records Category for phages, 1055 entries, 1563756 bases FILE.056 ddbjphg.acc 1240 records FILE.057 ddbjphg.aut 4098 records FILE.058 ddbjphg.dir 1055 records FILE.059 ddbjphg.idx 1056 records FILE.060 ddbjphg.jou 1687 records FILE.061 ddbjphg.key 4822 records FILE.062 ddbjphg.org 1055 records FILE.063 ddbjphg.sdr 1055 records FILE.064 ddbjphg.seq 68321 records Category for plants, 32480 entries, 42579726 bases FILE.065 ddbjpln.acc 34364 records FILE.066 ddbjpln.aut 111446 records FILE.067 ddbjpln.dir 32480 records FILE.068 ddbjpln.idx 32481 records FILE.069 ddbjpln.jou 46061 records FILE.070 ddbjpln.key 141396 records FILE.071 ddbjpln.org 32480 records FILE.072 ddbjpln.sdr 32480 records FILE.073 ddbjpln.seq 1926988 records Category for primates, 38563 entries, 37598826 bases FILE.074 ddbjpri.acc 43105 records FILE.075 ddbjpri.aut 174433 records FILE.076 ddbjpri.dir 38563 records FILE.077 ddbjpri.idx 38564 records FILE.078 ddbjpri.jou 55806 records FILE.079 ddbjpri.key 169411 records FILE.080 ddbjpri.org 38563 records FILE.081 ddbjpri.sdr 38563 records FILE.082 ddbjpri.seq 2122556 records Category for RNAs, 4864 entries, 2506517 bases FILE.083 ddbjrna.acc 5180 records FILE.084 ddbjrna.aut 19965 records FILE.085 ddbjrna.dir 4864 records FILE.086 ddbjrna.idx 4865 records FILE.087 ddbjrna.jou 6131 records FILE.088 ddbjrna.key 20394 records FILE.089 ddbjrna.org 4864 records FILE.090 ddbjrna.sdr 4864 records FILE.091 ddbjrna.seq 188814 records Category for rodents, 24728 entries, 27292972 bases FILE.092 ddbjrod.acc 28638 records FILE.093 ddbjrod.aut 101013 records FILE.094 ddbjrod.dir 24728 records FILE.095 ddbjrod.idx 24729 records FILE.096 ddbjrod.jou 34714 records FILE.097 ddbjrod.key 108047 records FILE.098 ddbjrod.org 24728 records FILE.099 ddbjrod.sdr 24728 records FILE.100 ddbjrod.seq 1385261 records Category for STS (sequence tagged site), 9195 entries, 2885759 bases FILE.101 ddbjsts.acc 9207 records FILE.102 ddbjsts.aut 39605 records FILE.103 ddbjsts.dir 9195 records FILE.104 ddbjsts.idx 9196 records FILE.105 ddbjsts.jou 12451 records FILE.106 ddbjsts.key 39729 records FILE.107 ddbjsts.org 9195 records FILE.108 ddbjsts.sdr 9195 records FILE.109 ddbjsts.seq 449391 records Category for synthetic DNAs, 9814 entries, 5013260 bases FILE.110 ddbjsyn.acc 9950 records FILE.111 ddbjsyn.aut 25954 records FILE.112 ddbjsyn.dir 9814 records FILE.113 ddbjsyn.idx 9815 records FILE.114 ddbjsyn.jou 10672 records FILE.115 ddbjsyn.key 39119 records FILE.116 ddbjsyn.org 9814 records FILE.117 ddbjsyn.sdr 9814 records FILE.118 ddbjsyn.seq 320020 records Category for unannotated sequences, 3601 entries, 926009 bases FILE.119 ddbjuna.acc 3616 records FILE.120 ddbjuna.aut 10737 records FILE.121 ddbjuna.dir 3601 records FILE.122 ddbjuna.idx 3602 records FILE.123 ddbjuna.jou 3705 records FILE.124 ddbjuna.key 14290 records FILE.125 ddbjuna.org 3601 records FILE.126 ddbjuna.sdr 3601 records FILE.127 ddbjuna.seq 95191 records Category for viruses, 21319 entries, 24681766 bases FILE.128 ddbjvrl.acc 22977 records FILE.129 ddbjvrl.aut 91341 records FILE.130 ddbjvrl.dir 21319 records FILE.131 ddbjvrl.idx 21320 records FILE.132 ddbjvrl.jou 31394 records FILE.133 ddbjvrl.key 94242 records FILE.134 ddbjvrl.org 21319 records FILE.135 ddbjvrl.sdr 21319 records FILE.136 ddbjvrl.seq 1177840 records Category for vertebrates other than mammals, primates, and rodents, 8374 entries, 9050584 bases FILE.137 ddbjvrt.acc 9217 records FILE.138 ddbjvrt.aut 30812 records FILE.139 ddbjvrt.dir 8374 records FILE.140 ddbjvrt.idx 8375 records FILE.141 ddbjvrt.jou 12433 records FILE.142 ddbjvrt.key 37231 records FILE.143 ddbjvrt.org 8374 records FILE.144 ddbjvrt.sdr 8374 records FILE.145 ddbjvrt.seq 453588 records Accession number index file FILE.146 ddbjacc.idx 285869 records Keyword phrase index file FILE.147 ddbjkey.idx 229261 records Author name index file FILE.148 ddbjaut.idx 871875 records Journal citation index file FILE.149 ddbjjou.idx 306616 records Gene name index file FILE.150 ddbjgen.idx 68227 records Japan Patent Information Organization sequence file 4551 entries. 3829577 bases FILE.151 japio.dat 214119 records