DNA Data Bank of Japan DNA Database Release 42, Jul. 2000, including 7,554,995 entries, 9,171,507,604 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 Jun. 29, 2000. 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", "AK", "AP", "AT", "AU", "AV", "BA" and "BB" have been collected and processed by DDBJ, and the rest have been prepared by GenBank and EMBL/EBI. 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, huge amounts of ESTs and quantities of genome sequences. 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. Incidentally, it is noted that the description of organella is changed from this release. The HUM division in this release is divided into four subdivisions in which 30,000 entries each are allocated except for the last one including the rest. 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 "AR", and those collected and supplied by EPO and EMBL/EBI respectively start with "A" and "AX". The entries with the prefixes "I","AR", "A","AX" 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 take no responsibility. In the present 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. Therefore, EST data were first sorted in terms of accession numbers this time, and then the result was divided into sets of 100,000 entries each except for the last set. The total number of sets this time is 47. 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 17 files; each of the first 16 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. HTGS in this release are distributed in eight files. First 23 files contain 3,000 entries each, and the last one contains the rest. 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. If you find an incorrect codon in a translated sequence, please let us know. The three data banks include the item VERSION in the flat file, which indicates a version of a submitted nucleotide sequence (see Table 1). It is expressed as AB123456.1, in which the digit(s) after the period is a version number. The reason for adding VERSION is that since a released 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 sequence is made public. Accordingly, the translated protein sequence will be accompanied with a /protein_id which is expressed as 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. We terminated the RNA division. The RNA data were redistributed according to the category of the organism. Therefore, you will find a human RNA sequence, for example, in the HUM division. The present release includes a division, CON. The CON division is to show the order of related sequences in a genome, and expressed by join and the accession numbers of the sequences. The contents of the CON division are compiled by the three data banks not by the data submitter. The current number of the entries of this division is 7,859. From the next release, we plan to include a new division, HTC (High Throughput cDNA). The definition of the HTC division is as follows. This division includes unfinished high throughput cDNA sequences, each of which has 5'UTR and 3'UTR at both ends and part of a coding region. The sequence may also include introns. When the sequence becomes finished later, it moves to the corresponding taxonomic division. The sequence is accompanied with a keyword, HTC (High Throughput cDNA), which is dropped when moved to a taxonomic division. This release was published by the following DDBJ staff. General administration T. Gojobori, M. Ota, Y. Fukuma, Y. Katsube, M. Maruyama, K. Okuda, J. Sugiyama, H. Tsutsui(hold), Y. Ueda, A. Watanabe Database construction Y. Tateno, S. Miyazaki, N. Asakawa, M. Ejima, M. Gojobori, A. Hasegawa, A. Hashizume, M. Hirashima, J. Mashima, N. Mukasa, M. Okaneya, A. Shimada, A. Suzuki, M. Suzuki, H. Tsutsui, T. Umezawa, Y. Yamamoto Database software development and management H. Sugawara, T. Imanishi, S. Miyazaki(hold), H. Harimoto, H. Hashimoto, T. Iizuka(hold), N. Ishizaka, K. Kaneda, T. Kato, Y. Kawanishi, K. Mamiya, S. Misu, Y. Minesaki, T. Mizunuma, T. Okayama, S. Sato, Y. Sugiyama, K. Suzuki, T. Takaki System management K. Nishikawa, K. Ikeo, N. Hoshi, T.Iizuka, I. Mochizuki, M. Nagura, T. Narita, T. Osawa, K. Yoshioka Editorial and public relations N. Saitou, K. Fukami-Kobayashi, Y. Daito, H. Ichikawa, K. Ichikawa, T. Kawamoto, S. Nagira 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 a firm friendship and an excellent collaboration with us. We also thank the Japanese Patent Office for a steady cooperation with us. The operation of DDBJ is supported by the Ministry of Education, Science, Sports and Culture, and we would gratefully note this here. DDBJ Database Release History Release Date Entries Bases Comments ------------------------------------------------------------------------------ 42 07/00 7,554,995 9,171,507,604 41 04/00 5,962,608 6,409,581,885 CON division started 40 01/00 5,388,125 4,762,696,173 RNA division eliminated 39 10/99 4,810,773 3,728,000,562 NID and PID discarded 38 07/99 4,294,369 3,098,519,597 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 eliminated 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 17 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 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 are created by the user by use of seq2indexes as mentioned in the release note. ------------------------------------------------------------------------------ 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 DDBJ 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 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) 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) 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) 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) COMMENT FEATURES Location/Qualifiers source 1..993 /organism="Escherichia coli" /sequenced_mol="cDNA to mRNA" /strain="W3110" CDS 1..810 /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 DDBJ style in the file 'ddbjbct.sdr'. The short directory file contains brief descriptions of all of the sequence entries contained in the DDBJ 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 four 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 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. ------------------------------------------------------------------------------ D00100 PSEASPAA BCT D00100 D00101 RABNP450R MAM D00101 D00102 HUMLTX HUM D00102 D00103 AFARRN5SA BCT D00103 AFRRN5SA BCT X05517 D00104 AFARRN5SB BCT D00104 AFRRN5SB BCT X05518 D00105 AFARRN5S BCT D00105 ASRRN5S BCT X05524 D00106 ACH5SRR BCT D00106 AXRRN5S BCT X05522 AXRRN5SA BCT X05523 D00107 ACH5SRRX BCT D00107 ACRRN5S BCT X05521 ------------------------------------------------------------------------------ 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 HUM M98056 ACTA BIOCHIM. BIOPHYS. SIN. 28, 233-239(1996) TKTII PLN X82230 ACTA BIOCHIM. POL. 24, 301-318 (1977) LUPTRFJ PLN K00345 LUPTRFN PLN K00346 ACTA BIOCHIM. POL. 26, 369-381(1979) HVTRNPHE PLN X02683 ACTA BIOCHIM. POL. 29, 143-149 (1982) EMEMTA PLN M32572 EMEMTB PLN M32573 EMEMTC PLN M32574 EMEMTD PLN M32575 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 923 records Category for bacteria, 81326 entries, 192142282 bases ddbjbct.seq 8290833 records Category for EST1 (expressed sequence tag), 100000 entries, 37317616 bases ddbjest1.seq 5955742 records Category for EST2 (expressed sequence tag), 100000 entries, 41136593 bases ddbjest2.seq 5828705 records Category for EST3 (expressed sequence tag), 100000 entries, 37308321 bases ddbjest3.seq 5775937 records Category for EST4 (expressed sequence tag), 100000 entries, 32463544 bases ddbjest4.seq 6021713 records Category for EST5 (expressed sequence tag), 100000 entries, 38755986 bases ddbjest5.seq 5745025 records Category for EST6 (expressed sequence tag), 100000 entries, 40191045 bases ddbjest6.seq 5632111 records Category for EST7 (expressed sequence tag), 100000 entries, 38981287 bases ddbjest7.seq 5665803 records Category for EST8 (expressed sequence tag), 100000 entries, 38773506 bases ddbjest8.seq 5678350 records Category for EST9 (expressed sequence tag), 100000 entries, 39112305 bases ddbjest9.seq 5680519 records Category for EST10 (expressed sequence tag), 100000 entries, 39351262 bases ddbjest10.seq 5651576 records Category for EST11 (expressed sequence tag), 100000 entries, 41943506 bases ddbjest11.seq 5753960 records Category for EST12 (expressed sequence tag), 100000 entries, 43593135 bases ddbjest12.seq 5653595 records Category for EST13 (expressed sequence tag), 100000 entries, 40488822 bases ddbjest13.seq 5292340 records Category for EST14 (expressed sequence tag), 100000 entries, 39898187 bases ddbjest14.seq 5555332 records Category for EST15 (expressed sequence tag), 100000 entries, 41431172 bases ddbjest15.seq 5814966 records Category for EST16 (expressed sequence tag), 100000 entries, 44382863 bases ddbjest16.seq 5789681 records Category for EST17 (expressed sequence tag), 100000 entries, 41154385 bases ddbjest17.seq 5611602 records Category for EST18 (expressed sequence tag), 100000 entries, 44413377 bases ddbjest18.seq 5766790 records Category for EST19 (expressed sequence tag), 100000 entries, 42090530 bases ddbjest19.seq 5846442 records Category for EST20 (expressed sequence tag), 100000 entries, 42338741 bases ddbjest20.seq 5601938 records Category for EST21 (expressed sequence tag), 100000 entries, 46291671 bases ddbjest21.seq 4511122 records Category for EST22 (expressed sequence tag), 100000 entries, 30250157 bases ddbjest22.seq 5492036 records Category for EST23 (expressed sequence tag), 100000 entries, 26040571 bases ddbjest23.seq 5629063 records Category for EST24 (expressed sequence tag), 100000 entries, 27402644 bases ddbjest24.seq 7730661 records Category for EST25 (expressed sequence tag), 100000 entries, 24750420 bases ddbjest25.seq 8795615 records Category for EST26 (expressed sequence tag), 100000 entries, 44413493 bases ddbjest26.seq 4755243 records Category for EST27 (expressed sequence tag), 100000 entries, 43653335 bases ddbjest27.seq 5572533 records Category for EST28 (expressed sequence tag), 100000 entries, 44281618 bases ddbjest28.seq 6052482 records Category for EST29 (expressed sequence tag), 100000 entries, 42980704 bases ddbjest29.seq 5882109 records Category for EST30 (expressed sequence tag), 100000 entries, 40268228 bases ddbjest30.seq 5568289 records Category for EST31 (expressed sequence tag), 100000 entries, 39182846 bases ddbjest31.seq 5948937 records Category for EST32 (expressed sequence tag), 100000 entries, 45170411 bases ddbjest32.seq 6091462 records Category for EST33 (expressed sequence tag), 100000 entries, 48009610 bases ddbjest33.seq 5650515 records Category for EST34 (expressed sequence tag), 100000 entries, 44261800 bases ddbjest34.seq 5693419 records Category for EST35 (expressed sequence tag), 100000 entries, 34773440 bases ddbjest35.seq 5710980 records Category for EST36 (expressed sequence tag), 100000 entries, 47705465 bases ddbjest36.seq 5096865 records Category for EST37 (expressed sequence tag), 100000 entries, 26005240 bases ddbjest37.seq 8664686 records Category for EST38 (expressed sequence tag), 100000 entries, 27675474 bases ddbjest38.seq 8659897 records Category for EST39 (expressed sequence tag), 100000 entries, 28365244 bases ddbjest39.seq 8611801 records Category for EST40 (expressed sequence tag), 100000 entries, 28047181 bases ddbjest40.seq 8427240 records Category for EST41 (expressed sequence tag), 100000 entries, 41843086 bases ddbjest41.seq 5711814 records Category for EST42 (expressed sequence tag), 100000 entries, 40991927 bases ddbjest42.seq 5669048 records Category for EST43 (expressed sequence tag), 100000 entries, 36855376 bases ddbjest43.seq 4264706 records Category for EST44 (expressed sequence tag), 100000 entries, 31488994 bases ddbjest44.seq 4875733 records Category for EST45 (expressed sequence tag), 100000 entries, 36153669 bases ddbjest45.seq 6129657 records Category for EST46 (expressed sequence tag), 100000 entries, 36711551 bases ddbjest46.seq 5928067 records Category for EST47 (expressed sequence tag), 100000 entries, 34951550 bases ddbjest47.seq 5767494 records Category for EST48 (expressed sequence tag), 100000 entries, 36654227 bases ddbjest48.seq 5893991 records Category for EST49 (expressed sequence tag), 90281 entries, 35593178 bases ddbjest49.seq 5350689 records Category for GSS1 (Genome Survey Sequence), 100000 entries, 64958741 bases ddbjgss1.seq 4703961 records Category for GSS2 (Genome Survey Sequence), 100000 entries, 81090025 bases ddbjgss2.seq 5622496 records Category for GSS3 (Genome Survey Sequence), 100000 entries, 88077807 bases ddbjgss3.seq 6011420 records Category for GSS4 (Genome Survey Sequence), 100000 entries, 40897337 bases ddbjgss4.seq 5086380 records Category for GSS5 (Genome Survey Sequence), 100000 entries, 46141393 bases ddbjgss5.seq 5133371 records Category for GSS6 (Genome Survey Sequence), 100000 entries, 49348730 bases ddbjgss6.seq 5327500 records Category for GSS7 (Genome Survey Sequence), 100000 entries, 52779858 bases ddbjgss7.seq 5565724 records Category for GSS8 (Genome Survey Sequence), 100000 entries, 49828404 bases ddbjgss8.seq 5680759 records Category for GSS9 (Genome Survey Sequence), 100000 entries, 50978568 bases ddbjgss9.seq 5742714 records Category for GSS10 (Genome Survey Sequence), 100000 entries, 50450986 bases ddbjgss10.seq 5886872 records Category for GSS11 (Genome Survey Sequence), 100000 entries, 56300773 bases ddbjgss11.seq 5854397 records Category for GSS12 (Genome Survey Sequence), 100000 entries, 53527905 bases ddbjgss12.seq 6036809 records Category for GSS13 (Genome Survey Sequence), 100000 entries, 49945441 bases ddbjgss13.seq 5786717 records Category for GSS14 (Genome Survey Sequence), 100000 entries, 45003692 bases ddbjgss14.seq 6011314 records Category for GSS15 (Genome Survey Sequence), 100000 entries, 56205280 bases ddbjgss15.seq 5636788 records Category for GSS16 (Genome Survey Sequence), 100000 entries, 50704028 bases ddbjgss16.seq 5539564 records Category for GSS17 (Genome Survey Sequence), 56764 entries, 25428620 bases ddbjgss17.seq 2888469 records Category for HTG1 (high throughput genomic sequencing), 3000 entries, 447402710 bases ddbjhtg1.seq 7845377 records Category for HTG2 (high throughput genomic sequencing), 3000 entries, 379294420 bases ddbjhtg2.seq 6692850 records Category for HTG3 (high throughput genomic sequencing), 3000 entries, 229635764 bases ddbjhtg3.seq 4140093 records Category for HTG4 (high throughput genomic sequencing), 3000 entries, 270985948 bases ddbjhtg4.seq 4755218 records Category for HTG5 (high throughput genomic sequencing), 3000 entries, 354764918 bases ddbjhtg5.seq 6272061 records Category for HTG6 (high throughput genomic sequencing), 3000 entries, 436622523 bases ddbjhtg6.seq 7778286 records Category for HTG7 (high throughput genomic sequencing), 3000 entries, 261972794 bases ddbjhtg7.seq 4708733 records Category for HTG8 (high throughput genomic sequencing), 3000 entries, 12505543 bases ddbjhtg8.seq 346822 records Category for HTG9 (high throughput genomic sequencing), 3000 entries, 31374774 bases ddbjhtg9.seq 674754 records Category for HTG10 (high throughput genomic sequencing), 3000 entries, 34934313 bases ddbjhtg10.seq 742652 records Category for HTG11 (high throughput genomic sequencing), 3000 entries, 27591871 bases ddbjhtg11.seq 611759 records Category for HTG12 (high throughput genomic sequencing), 3000 entries, 2624931 bases ddbjhtg12.seq 171213 records Category for HTG13 (high throughput genomic sequencing), 3000 entries, 35603566 bases ddbjhtg13.seq 752149 records Category for HTG14 (high throughput genomic sequencing), 3000 entries, 11746722 bases ddbjhtg14.seq 331315 records Category for HTG15 (high throughput genomic sequencing), 3000 entries, 11081351 bases ddbjhtg15.seq 318875 records Category for HTG16 (high throughput genomic sequencing), 3000 entries, 42666131 bases ddbjhtg916seq 873810 records Category for HTG17 (high throughput genomic sequencing), 3000 entries, 10034650 bases ddbjhtg17.seq 299617 records Category for HTG18 (high throughput genomic sequencing), 3000 entries, 29598339 bases ddbjhtg18.seq 645755 records Category for HTG19 (high throughput genomic sequencing), 3000 entries, 25970980 bases ddbjhtg19.seq 572796 records Category for HTG20 (high throughput genomic sequencing), 3000 entries, 60023972 bases ddbjhtg20.seq 1181647 records Category for HTG21 (high throughput genomic sequencing), 3000 entries, 197175786 bases ddbjhtg21.seq 3604467 records Category for HTG22 (high throughput genomic sequencing), 3000 entries, 168776601 bases ddbjhtg22.seq 3053580 records Category for HTG23 (high throughput genomic sequencing), 3000 entries, 495515007 bases ddbjhtg23.seq 8652729 records Category for HTG24 (high throughput genomic sequencing), 2969 entries, 457865810 bases ddbjhtg24.seq 8064761 records Category for human1, 30000 entries, 442439777 bases ddbjhum1.seq 9773029 records Category for human2, 30000 entries, 313758014 bases ddbjhum2.seq 7478758 records Category for human3, 30000 entries, 43669130 bases ddbjhum3.seq 2076631 records Category for human4, 29272 entries, 55428563 bases ddbjhum4.seq 2233435 records Category for invertebrates, 68376 entries, 336344524 bases ddbjinv.seq 9557866 records Category for mammals, 25052 entries, 22128600 bases ddbjmam.seq 1405460 records Category for patents, 205856 entries, 66504878 bases ddbjpat.seq 5554432 records Category for phages, 1565 entries, 4234873 bases ddbjphg.seq 189754 records Category for plants, 113117 entries, 302978541 bases ddbjpln.seq 10773247 records Category for primates, 8074 entries, 6531301 bases ddbjpri.seq 437252 records Category for rodents, 56597 entries, 89487897 bases ddbjrod.seq 4039395 records Category for STS (sequence tagged site), 115403 entries, 50619293 bases ddbjsts.seq 6613135 records Category for synthetic DNAs, 3788 entries, 9447294 bases ddbjsyn.seq 341276 records Category for unannotated sequences, 480 entries, 291337 bases ddbjuna.seq 21903 records Category for viruses, 95438 entries, 82758844 bases ddbjvrl.seq 5756417 records Category for vertebrates, 41637 entries, 38619640 bases ddbjvrt.seq 2374244 records Accession number index file ddbjacc.idx 7580995 records Keyword phrase index file ddbjkey.idx 2837826 records Journal citation index file ddbjjou.idx 4395901 records Gene name index file ddbjgen.idx 475580 records