DNA Data Bank of Japan DNA Database Release 10, January 1992, including 59,233 entries, 77,701,394 bases. This database may be copied and redistributed without permission, on the condition that all the statements in the followings are reproduced with each copy. Unlike past releases, this release contains the newest data prepared by DDBJ, GenBank, and the EMBL Data Library as of January, 1992. Thanks to international collaboration between the three data banks, the International Nucleotide Sequence Database was organized, resulting in a unified database published in this release. All the entries designated by the accession numbers with a "D" have been collected and processed by DDBJ, and the rest have been prepared by GenBank and the EMBL Data Library. It is particularly noted that for an unavoidable problem existing at present some entries in the three databases overlap. We apologize for this, and will resolve the problem by working together with the other data banks. Because the release contains unified data, all the entries have been annotated with common feature keys. The feature keys used in the previous release were updated beforehand. The present release was prepared by processing the data on the relational data base management system (Sybase). It does not include amino acid sequence data, because the genetic code system is known to be no longer uniform among the species and organella, and the International Nucleotide Sequence Database is not yet prepared for this. Published by: Y. Ugawa, Y. Yamazaki, M. Horie, M. Iwase, M. Saito, Y. Sato, S. Suzuki, Y. Hasegawa, Y. Hattori, Y. Noguchi, M. Shimoyama, E. Hatada, R. Suzuki, R. Uchida, Y. Shidahara, Y. Matsushima, A. Watanabe, Y. Ueda, M. Nakaoka, T. Kawamoto, H. Kitakami, N. Saitou, Y. Tateno, and T. Gojobori DNA Data Bank of Japan National Institute of Genetics Mishima 411, Japan Phone: +81 559 75 0771 FAX: +81 559 75 6040 E-mail: ddbj@ddbj.nig.ac.jp Acknowledgement: We are grateful to GenBank and the EMBL Data Library for permitting us to include their data in the present release. We also thank Michael Cinkosky and Gifford Keen of GenBank for their help in installing the DDBJ database into the relational database management system. Our thanks are extended to David Lipman, Director of NCBI, for his valuable advice. This release covers 13 categories of organisms and others as follows: ------------------------------------------------------------------------------ ddbjbct.*** Category for bacteria ddbjinv.*** Category for invertebrates ddbjmam.*** Category for mammals ddbjorg.*** Category for organella ddbjphg.*** Category for phages ddbjpln.*** Category for plants ddbjpri.*** Category for primates ddbjrna.*** Category for RNAs ddbjrod.*** Category for rodents 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 eight files. Note that all the files except for *******.seq 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. ------------------------------------------------------------------------------ *******.seq List of an entry in DDBJ format, see Table 1 for details *******.acc List of the accession numbers, see Table 2 for details *******.aut List of the authors, see Table 3 for details *******.dir List of the short directory, see Table 4 for details *******.idx List of indices, see Table 5 for details *******.jou List of the journals, see Table 6 for details *******.key List of the key words, see Table 7 for details *******.org List of the species names, see Table 8 for details ------------------------------------------------------------------------------ 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 number. ------------------------------------------------------------------------------ D00001 -> ECOPBPAA X04516 D00002 -> ECOPYRH X04469 D00006 -> PNS981TET D00006 D00038 -> BRLAM330 D00038 D00066 -> BAC139AC D00066 D00067 -> ECONANA M20207 D00069 -> ECOUVRD2 D00069 D00087 -> BACXYNAA D00087 D00112 -> MSGRRN5S X05526 D00117 -> BACHDCRY D00117 ------------------------------------------------------------------------------ Table 3. Part of the contents in the file 'ddbjbct.aut'. For each author name given in the first column, the locus name and primary accession number are listed. They are arranged in the alphabetical order of the author name. ------------------------------------------------------------------------------ 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 contents in the file 'ddbjbct.dir'. For each locus name given in the first column, the 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 name. ------------------------------------------------------------------------------ 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. ACCAAC2 M62833 ds-DNA 1123 Acinetobacter baumannii aminoglycoside acetyltransferase (aac2) gene, complete cds. ACCACEAA M62822 ds-DNA 1874 A.baumannii chloramphenicol acetyltransferase (cat) gene, complete cds. ACCAPHA6 X07753 ds-DNA 1170 Acinetobacter baumannii aphA-6 gene. ------------------------------------------------------------------------------ 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 name. ------------------------------------------------------------------------------ %***************************** #ABCAARAA 0 3211 #ABCADHCC 3212 10608 #ABCALDH 10609 15864 #ABCBCSAA 15865 29583 #ABCCELA 29584 32289 #ABCCELSYN 32290 40960 #ABCIS1380 40961 44711 #ACCAAC2 44712 47749 #ACCACEAA 47750 51050 ------------------------------------------------------------------------------ Table 6. Part of the contents in the file 'ddbjbct.jou'. Information on the journal is given in which the 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) -> ERWPALI D00217 ------------------------------------------------------------------------------ Table 7. Part of the contents in the file 'ddbjbct.key'. For the locus and accession number given on the right of the arrow, 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 given on the right of the arrow, the species names of the organism are listed from which the nucleotide sequence was obtained. They are arranged in the alphabetical order of the species name. ------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------ The files in this release are arranged in the following order on tapes with non-labeled format. Release note FILE.001 ddbjrel.txt Category for bacteria, 6746 entries, 11544280 bases FILE.002 ddbjbct.acc FILE.003 ddbjbct.aut FILE.004 ddbjbct.dir FILE.005 ddbjbct.idx FILE.006 ddbjbct.jou FILE.007 ddbjbct.key FILE.008 ddbjbct.org FILE.009 ddbjbct.seq Category for invertebrates, 4923 entries, 6829021 bases FILE.010 ddbjinv.acc FILE.011 ddbjinv.aut FILE.012 ddbjinv.dir FILE.013 ddbjinv.idx FILE.014 ddbjinv.jou FILE.015 ddbjinv.key FILE.016 ddbjinv.org FILE.017 ddbjinv.seq Category for mammals, 2329 entries, 2996983 bases FILE.018 ddbjmam.acc FILE.019 ddbjmam.aut FILE.020 ddbjmam.dir FILE.021 ddbjmam.idx FILE.022 ddbjmam.jou FILE.023 ddbjmam.key FILE.024 ddbjmam.org FILE.025 ddbjmam.seq Category for organella, 1952 entries, 3135042 bases FILE.026 ddbjorg.acc FILE.027 ddbjorg.aut FILE.028 ddbjorg.dir FILE.029 ddbjorg.idx FILE.030 ddbjorg.jou FILE.031 ddbjorg.key FILE.032 ddbjorg.org FILE.033 ddbjorg.seq Category for phages, 748 entries, 1097928 bases FILE.034 ddbjphg.acc FILE.035 ddbjphg.aut FILE.036 ddbjphg.dir FILE.037 ddbjphg.idx FILE.038 ddbjphg.jou FILE.039 ddbjphg.key FILE.040 ddbjphg.org FILE.041 ddbjphg.seq Category for plants, 5094 entries, 8533114 bases FILE.042 ddbjpln.acc FILE.043 ddbjpln.aut FILE.044 ddbjpln.dir FILE.045 ddbjpln.idx FILE.046 ddbjpln.jou FILE.047 ddbjpln.key FILE.048 ddbjpln.org FILE.049 ddbjpln.seq Category for primates, 11759 entries, 14035626 bases FILE.050 ddbjpri.acc FILE.051 ddbjpri.aut FILE.052 ddbjpri.dir FILE.053 ddbjpri.idx FILE.054 ddbjpri.jou FILE.055 ddbjpri.key FILE.056 ddbjpri.org FILE.057 ddbjpri.seq Category for RNAs, 2228 entries, 947599 bases FILE.058 ddbjrna.acc FILE.059 ddbjrna.aut FILE.060 ddbjrna.dir FILE.061 ddbjrna.idx FILE.062 ddbjrna.jou FILE.063 ddbjrna.key FILE.064 ddbjrna.org FILE.065 ddbjrna.seq Category for rodents, 11279 entries, 12300726 bases FILE.066 ddbjrod.acc FILE.067 ddbjrod.aut FILE.068 ddbjrod.dir FILE.069 ddbjrod.idx FILE.070 ddbjrod.jou FILE.071 ddbjrod.key FILE.072 ddbjrod.org FILE.073 ddbjrod.seq Category for synthetic DNAs, 1240 entries, 780135 bases FILE.074 ddbjsyn.acc FILE.075 ddbjsyn.aut FILE.076 ddbjsyn.dir FILE.077 ddbjsyn.idx FILE.078 ddbjsyn.jou FILE.079 ddbjsyn.key FILE.080 ddbjsyn.org FILE.081 ddbjsyn.seq Category for unannotated sequences, 2104 entries, 1921841 bases FILE.082 ddbjuna.acc FILE.083 ddbjuna.aut FILE.084 ddbjuna.dir FILE.085 ddbjuna.idx FILE.086 ddbjuna.jou FILE.087 ddbjuna.key FILE.088 ddbjuna.org FILE.089 ddbjuna.seq Category for viruses, 5963 entries, 10163693 bases FILE.090 ddbjvrl.acc FILE.091 ddbjvrl.aut FILE.092 ddbjvrl.dir FILE.093 ddbjvrl.idx FILE.094 ddbjvrl.jou FILE.095 ddbjvrl.key FILE.096 ddbjvrl.org FILE.097 ddbjvrl.seq Category for vertebrates other than mammals, primates, and rodents, 2868 entries, 3415406 bases FILE.098 ddbjvrt.acc FILE.099 ddbjvrt.aut FILE.100 ddbjvrt.dir FILE.101 ddbjvrt.idx FILE.102 ddbjvrt.jou FILE.103 ddbjvrt.key FILE.104 ddbjvrt.org FILE.105 ddbjvrt.seq DNA data submission form FILE.106 ddbjsub.txt