DNA Data Bank of Japan DNA Database Release 37, Mar. 1999, including 3,311,627 entries, 2,375,261,951 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 the DNA Data Bank of Japan (DDBJ), GenBank, and European Molecular Biology Laboratory/European Bioinformatics Institute (EMBL/EBI) as of Feb. 16, 1999. This unified database was made possible thanks to the international collaboration among the three data banks. All the entries have accordingly been annotated with the feature keys common to them. All the entries designated by the accession numbers with the prefixes "C", "D", "E", "AB", "AG", "AP", "AT" and "AU" have been collected and processed by DDBJ, and the rest have been prepared by GenBank and EMBL/EBI. Since the content of a nucleotide sequence is often revised due to replacements, additions and deletions of bases made by the submitter, the accession number sometimes does not work to tell which sequence is really in question. Thus, an additional identifier was introduced to specify a particular sequence in a series of revised sequences. This identifier is called NID. For the same reason for translated amino acid sequences, PID was brought into being. There have been a number of genome projects going on worldwide. Among them human genome projects have probably been most productive and yielded a large number of ordinary sequences and huge amounts of ESTs. Thus, we have the human (HUM) division solely for human sequences and the primate (PRI) division for non-human primate sequences. Note that the EST division also contains human sequences. The present release does not have the ORG division. Thus, if you are interested in human mitochondrial sequences, for example, you are now advised to refer to the HUM division. This release also includes an independent division (PAT) for patent data. The patent data are those which the Japanese Patent Office (JPO), United States Patent and Trademark Office (USPTO), and the European Patent Office (EPO) collected and processed. The accession numbers of the patent data collected by the Japanese Patent Office start with the prefix "E", those collected and supplied by USPTO and GenBank respectively start with "I", and those collected and supplied by EPO and EMBL/EBI respectively start with "A". The entries with the prefixes "I", "A" and "E" were allocated to a file (ddbjpat.seq) in the DDBJ format. Note also that unauthorized use of the patent data may cause legal issues for which we have no responsibility. In this release, the SOURCE in the flat file was revisited and revised if necessary in accordance with the unified taxonomy database common to the three data banks. The number of ESTs has been increasing at an enormous rate and is expected to be growing even more rapidly in the future. To cope with this situation and handle the data files with least possible time and manner, we split the EST data in eighteen files in the present release; ddbjest1 for entries with the accession numbers with A to M prefixes, ddbjest2 for those with N to S, ddbjest3 for those with T to Z, and ddbjest4 to ddbjest18 contain those with two letter prefixes. The files from the 4th to 17th contain 100,000 entries each, and the 18th one does the rest. The present release includes the GSS division. GSS stands for the Genome Survey Sequence, which is similar to EST, except that GSS is genomic DNA whereas EST is cDNA. This division is divided into six files; each of the first five files contains 100,000 entries and the last one does the rest. This release also includes the High Throughput Genome Sequence (HTGS) which comes mainly from genome project teams which deal with a clone as a sequencing unit. The index files are not presented in this release except for ddbjacc.idx, ddbjgen.idx, ddbjjou.idx, and ddbjkey.idx. Instead, we have included a program by which to make the index files not presented in this release. For the use of the program, see the files, seq2indexes.doc, seq2indexes.c, and seq2indexes.h in this release. The present release contains amino acid sequences that were translated from the corresponding nucleotide sequences in our database. In the translation we paid much attention to the fact that some species or organella have a codon different from the universal one, and used the proper codon table. However, if you find an incorrect codon in a translated sequence, please let us know. As announced in the previous release note, from this release, the three data banks add a new item VERSION in the flat file, which indicates a version of a submitted nucleotide sequence (see Table 1). It is expressed like AB123456.1, in which the digit(s) after the period is a version number. The reason for adding VERSION is that since a submitted sequence sometimes revised by the submitter, the accession number alone cannot specify the sequence in question causing the user a trouble. The number is increased by one every time when a revised sequences made public. Accordingly, the translated protein sequence will be accompanied with a /protein_id which is expressed like BAA12345.1, in which the digit(s) after the period is again a version number. The number is increased by one when the corresponding nucleotide sequence is revised and the protein sequence is changed as a result, and when the revised protein sequence is made public. To implement the new numbers synchronously among the three data banks, we issued this release earlier than the ordinarily scheduled time. The present NID and PID will be not in use in the near future. This release was published by the following DDBJ staff. General administration T. Gojobori, T. Imanishi, Y. Fukuma, A. Watanabe, Y. Ueda, Y. Katsube, K. Okuda, J. Sugiyama, J. Bellgard, H. Tsutsui(hold), Y. Noguchi, R. Chapman Database construction Y. Tateno, M. Ota, S. Miyazaki(hold), N. Yasuda, Y. Sato, H. Tsutsui, C. Hamamatsu, M. Hirashima, A. Hasegawa, A. Suzuki, Y. Yamamoto, M. Ejima, M. Okaneya, N. Endo, M. Iwase, R. Suzuki, R. Uchida, Y. Shidahara, M. Gojobori, K. Nomura, M. Imma, J. Muroya, N. Ohkubo, A. Shimada Database software development and management H. Sugawara, S. Miyazaki, T. Okayama, S. Misu, T. Mizunuma, Y. Kawanishi, K. Goto, Y. Fukuma(hold), M. Kikuchi(hold), T. Futatsuki, H. Hashimoto, H. Harimoto, T. Horiguchi, Y. Minesaki, R. Tanabe, H. Yamamoto, K. Mamiya, T. Takaki, S. Sato, H. Ichinose System management K. Nishikawa, K. Ikeo, T. Ito, A. Murakami, I. Mochizuki, M. Kikuchi, T. Narita, M. Nagura Editorial and public relations N. Saitou, K. Fukami-Kobayashi, M. Horie, Y. Daito, Y. Hattori, T. Kawamoto, S. Nagira, K. Ichikawa 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) ddbjsub@ddbj.nig.ac.jp (for data submission) ddbjupdt@ddbj.nig.ac.jp (for updates and notification of publication) WWW: http://www.ddbj.nig.ac.jp (for DDBJ WWW server) http://sakura.ddbj.nig.ac.jp (for DDBJ sequence data submission system SAKURA) Acknowledgement: We are grateful to NCBI and EMBL/EBI for permitting us to include the data they have collected and processed in the present release. We also thank the Japanese Patent Office for kindly allowing us to distribute the patent data they collected and processed. DDBJ Database Release History Release Date Entries Bases Comments ------------------------------------------------------------------------ 37 03/99 3,311,627 2,375,261,951 VERSION, /protein_id started 36 01/99 3,073,166 2,190,425,560 35 10/98 2,759,261 1,957,341,169 34 07/98 2,412,785 1,708,580,623 33 04/98 2,174,769 1,479,303,279 32 01/98 1,956,669 1,300,950,613 31 10/97 1,731,532 1,139,869,464 Adoption of the unified taxonomy database 30 07/97 1,534,115 992,788,339 NID and PID started 29 04/97 1,270,194 841,415,232 28 01/97 1,154,120 756,785,219 HTG division started ORG division eliminated 27 10/96 936,697 608,103,057 GSS division started 26 07/96 835,552 551,932,448 25 04/96 744,490 499,300,364 /translation started 24 01/96 637,508 431,771,652 23 10/95 569,757 390,694,350 22 07/95 437,588 322,982,425 HUM division started 21 04/95 274,596 250,875,023 20 01/95 239,689 231,299,557 19 10/94 204,332 205,274,131 18 07/94 185,230 192,473,021 17 04/94 169,957 179,942,209 16 01/94 154,626 165,017,628 15 10/93 131,649 147,224,690 14 07/93 120,350 138,686,333 13 04/93 112,067 129,784,445 12 01/93 97,683 120,815,244 EST division started 11 07/92 65,693 84,839,075 10 01/92 59,317 77,805,556 GenBank/EMBL inclusion started 9 07/91 1,130 2,002,124 8 01/91 879 1,573,442 7 07/90 681 1,154,211 6 01/90 496 841,236 5 07/89 395 679,378 4 01/89 302 535,985 3 07/88 230 345,850 2 01/88 142 199,392 1 07/87 66 108,970 Started with DDBJ only ------------------------------------------------------------------------ This release covers 18 categories of organisms and others as follows: ------------------------------------------------------------------------------ ddbjbct.*** Category for bacteria ddbjest.*** Category for EST (expressed sequence tag) ddbjhtg.*** Category for HTG (high throughput genomic sequencing) ddbjhum.*** Category for human ddbjgss.*** Category for GSS (Genome Survey Sequence) ddbjinv.*** Category for invertebrates ddbjmam.*** Category for mammals other than primates and rodents ddbjpat.*** Category for patents ddbjphg.*** Category for phages ddbjpln.*** Category for plants ddbjpri.*** Category for primates other than human 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 ------------------------------------------------------------------------------ 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 D87069 993 bp mRNA BCT 07-FEB-1999 DEFINITION Escherichia coli mRNA for RNA polymerase sigma subunit, truncated form of sigma-38, complete cds. ACCESSION D87069 NID d1070184 VERSION D87069.1 KEYWORDS RNA polymerase sigma subunit, truncated form of sigma-38. SOURCE Escherichia coli (strain:W3110) cDNA to mRNA. ORGANISM Escherichia coli Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 993) AUTHORS Jishage,M. TITLE Direct Submission JOURNAL Submitted (14-AUG-1996) to the DDBJ/EMBL/GenBank databases. Miki Jishage, National Institute of Genetics, Molecular Genetics; Yata 1111, Mishima, Shizuoka 411, Japan (E-mail:mjishage@lab.nig.ac.jp, Tel:0559-81-6742, Fax:0559-81-6746) STANDARD full staff_review REFERENCE 2 (bases 1 to 993) AUTHORS Jishage,M. and Ishihama,A. TITLE Variation in RNA polymerase sigma subunit composition within different stocks of Escherichia coli starin W3110 JOURNAL Unpublished (1996) STANDARD full staff_review REFERENCE 3 (sites) AUTHORS Ivanova,A., Renshaw,M., Guntaka,R. and Eisenstark,A. TITLE DNA base sequence variability in katF (putative sigma factor) gene Escherichia coli JOURNAL Nucleic Acids Res. 20, 5479-5480 (1992) STANDARD full staff_review REFERENCE 4 (sites) AUTHORS Takayanagi,Y., Tanaka,K. and Takahashi,H. TITLE Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli JOURNAL Mol Gen Genet 243, 525-531 (1994) STANDARD full staff_review COMMENT FEATURES Location/Qualifiers source 1..993 /organism="Escherichia coli" /sequenced_mol="cDNA to mRNA" /strain="W3110" CDS 1..810 /db_xref="PID:d1013928" /note="the gene has four single base changes, resulting in two amino acid substitutions and an amber mutation" /product="RNA polymerase sigma subunit, truncated form of sigma-38" /protein_id="BAA13238.1" /translation="MSQNTLKVHDLNEDAEFDENGVEVFDEKALVEYEPSDNDLAEEE LLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLV VKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN QTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK" /transl_table=11 mutation 75 /citation=[3] /replace="t" mutation 97 /citation=[3] /replace="t" mutation 99 /citation=[3] /replace="t" mutation 808 /citation=[3] /replace="t" BASE COUNT 254 a 223 c 291 g 225 t 0 others ORIGIN 1 atgagtcaga atacgctgaa agttcatgat ttaaatgaag atgcggaatt tgatgagaac 61 ggagttgagg tttttgacga aaaggcctta gtagaatatg aacccagtga taacgatttg 121 gccgaagagg aactgttatc gcagggagcc acacagcgtg tgttggacgc gactcagctt 181 taccttggtg agattggtta ttcaccactg ttaacggccg aagaagaagt ttattttgcg 241 cgtcgcgcac tgcgtggaga tgtcgcctct cgccgccgga tgatcgagag taacttgcgt 301 ctggtggtaa aaattgcccg ccgttatggc aatcgtggtc tggcgttgct ggaccttatc 361 gaagagggca acctggggct gatccgcgcg gtagagaagt ttgacccgga acgtggtttc 421 cgcttctcaa catacgcaac ctggtggatt cgccagacga ttgaacgggc gattatgaac 481 caaacccgta ctattcgttt gccgattcac atcgtaaagg agctgaacgt ttacctgcga 541 accgcacgtg agttgtccca taagctggac catgaaccaa gtgcggaaga gatcgcagag 601 caactggata agccagttga tgacgtcagc cgtatgcttc gtcttaacga gcgcattacc 661 tcggtagaca ccccgctggg tggtgattcc gaaaaagcgt tgctggacat cctggccgat 721 gaaaaagaga acggtccgga agataccacg caagatgacg atatgaagca gagcatcgtc 781 aaatggctgt tcgagctgaa cgccaaatag cgtgaagtgc tggcacgtcg attcggtttg 841 ctggggtacg aagcggcaac actggaagat gtaggtcgtg aaattggcct cacccgtgaa 901 cgtgttcgcc agattcaggt tgaaggcctg cgccgtttgc gcgaaatcct gcaaacgcag 961 gggctgaata tcgaagcgct gttccgcgag taa // ------------------------------------------------------------------------------ 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 ddbjrel.txt 762 records Category for bacteria, 54199 entries, 133124032 bases ddbjbct.seq 5822424 records Category for EST1 (expressed sequence tag), 280082 entries, 97699959 bases ddbjest1.seq 14777927 records Category for EST2 (expressed sequence tag), 178588 entries, 65474371 bases ddbjest2.seq 11002619 records Category for EST3 (expressed sequence tag), 215943 entries, 80209486 bases ddbjest3.seq 12614576 records Category for EST4 (expressed sequence tag), 100000 entries, 37323377 bases ddbjest4.seq 6086798 records Category for EST5 (expressed sequence tag), 100000 entries, 41141056 bases ddbjest5.seq 5983967 records Category for EST6 (expressed sequence tag), 100000 entries, 37300681 bases ddbjest6.seq 6028411 records Category for EST7 (expressed sequence tag), 100000 entries, 32462843 bases ddbjest7.seq 6245303 records Category for EST8 (expressed sequence tag), 100000 entries, 38755120 bases ddbjest8.seq 6016934 records Category for EST9 (expressed sequence tag), 100000 entries, 40190676 bases ddbjest9.seq 5939557 records Category for EST10 (expressed sequence tag), 100000 entries, 38979091 bases ddbjest10.seq 5938137 records Category for EST11 (expressed sequence tag), 100000 entries, 38770434 bases ddbjest11.seq 5965946 records Category for EST12 (expressed sequence tag), 100000 entries, 39127203 bases ddbjest12.seq 5946115 records Category for EST13 (expressed sequence tag), 100000 entries, 38788225 bases ddbjest13.seq 5909848 records Category for EST14 (expressed sequence tag), 100000 entries, 42111282 bases ddbjest14.seq 5939888 records Category for EST15 (expressed sequence tag), 100000 entries, 42882792 bases ddbjest15.seq 5954539 records Category for EST16 (expressed sequence tag), 100000 entries, 40268241 bases ddbjest16.seq 5569363 records Category for EST17 (expressed sequence tag), 100000 entries, 40950366 bases ddbjest17.seq 5785621 records Category for EST18 (expressed sequence tag), 92224 entries, 39976563 bases ddbjest18.seq 4976917 records Category for GSS1 (Genome Survey Sequence), 100000 entries, 48560099 bases ddbjgss1.seq 4811428 records Category for GSS2 (Genome Survey Sequence), 100000 entries, 41195177 bases ddbjgss2.seq 5053169 records Category for GSS3 (Genome Survey Sequence), 100000 entries, 48308206 bases ddbjgss3.seq 5202085 records Category for GSS4 (Genome Survey Sequence), 100000 entries, 51953303 bases ddbjgss4.seq 5568733 records Category for GSS5 (Genome Survey Sequence), 100000 entries, 48662222 bases ddbjgss5.seq 5308952 records Category for GSS6 (Genome Survey Sequence), 18245 entries, 8519628 bases ddbjgss6.seq 858905 records Category for HTG (high throughput genomic sequencing), 1758 entries, 241834192 bases ddbjhtg.seq 4133394 records Category for human, 91121 entries, 358634878 bases ddbjhum.seq 10878989 records Category for invertebrates, 41925 entries, 158325369 bases ddbjinv.seq 4992398 records Category for mammals, 17687 entries, 16485760 bases ddbjmam.seq 1040844 records Category for patents, 134612 entries, 42349047 bases ddbjpat.seq 3811049 records Category for phages, 1394 entries, 3033907 bases ddbjphg.seq 147987 records Category for plants, 68570 entries, 155968956 bases ddbjpln.seq 6135870 records Category for primates, 4977 entries, 3800669 bases ddbjpri.seq 276857 records Category for RNAs, 4883 entries, 2480449 bases ddbjrna.seq 204799 records Category for rodents, 45407 entries, 64541563 bases ddbjrod.seq 3193355 records Category for STS (sequence tagged site), 64115 entries, 22573045 bases ddbjsts.seq 3823501 records Category for synthetic DNAs, 3238 entries, 7336707 bases ddbjsyn.seq 277157 records Category for unannotated sequences, 785 entries, 652152 bases ddbjuna.seq 39569 records Category for viruses, 65827 entries, 59257968 bases ddbjvrl.seq 4124784 records Category for vertebrates, 26047 entries, 25252856 bases ddbjvrt.seq 1554471 records Accession number index file ddbjacc.idx 3331500 records Keyword phrase index file ddbjkey.idx 1325679 records Journal citation index file ddbjjou.idx 1861823 records Gene name index file ddbjgen.idx 300034 records