{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T07:56:21Z","timestamp":1761292581711},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,12,1]],"date-time":"2008-12-01T00:00:00Z","timestamp":1228089600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1186\/1471-2105-9-544","type":"journal-article","created":{"date-parts":[[2008,12,17]],"date-time":"2008-12-17T19:14:10Z","timestamp":1229541250000},"source":"Crossref","is-referenced-by-count":23,"title":["AnEnPi: identification and annotation of analogous enzymes"],"prefix":"10.1186","volume":"9","author":[{"given":"Thomas D","family":"Otto","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana Carolina R","family":"Guimar\u00e3es","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wim M","family":"Degrave","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio B","family":"de Miranda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,12,17]]},"reference":[{"key":"2529_CR1","unstructured":"Nomenclature Committee of the International Union of Biochemistry[ http:\/\/www.chem.qmul.ac.uk\/iubmb\/ ]"},{"issue":"50","key":"2529_CR2","doi-asserted-by":"publisher","first-page":"16487","DOI":"10.1021\/ja0466457","volume":"126","author":"M Kotera","year":"2004","unstructured":"Kotera M, Okuno Y, Hattori M, Goto S, Kanehisa M: Computational Assignment of the EC Numbers for Genomic-Scale Analysis of Enzymatic Reactions. Journal of the American Chemical Society 2004, 126(50):16487\u201316498.","journal-title":"Journal of the American Chemical Society"},{"key":"2529_CR3","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389\u20133402.","journal-title":"Nucleic Acids Res"},{"key":"2529_CR4","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological sequence analysis: probabilistic models of protein and nucleic acids","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy SR, Krogh A, Mitcison G: Biological sequence analysis: probabilistic models of protein and nucleic acids. Cambridge Uiversity Press; 1998."},{"key":"2529_CR5","first-page":"1","volume":"11","author":"JA Papin","year":"2003","unstructured":"Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO: Towards quantitative biology: Integration of biological information to elucidate disease pathways and to guide drug discovery. Biotechnology Annual Review 2003, 11: 1\u201368.","journal-title":"Biotechnology Annual Review"},{"issue":"2","key":"2529_CR6","doi-asserted-by":"publisher","first-page":"99","DOI":"10.2307\/2412448","volume":"19","author":"WM Fitch","year":"1970","unstructured":"Fitch WM: Distinguishing homologous from analogous proteins. Systematic Zoology 1970, 19(2):99\u2013113.","journal-title":"Systematic Zoology"},{"key":"2529_CR7","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1101\/gr.8.8.779","volume":"8","author":"MY Galperin","year":"1998","unstructured":"Galperin MY, Walker DR, Koonin EV: Analogous enzymes: independent inventions in enzyme evolution. Genome Res 1998, 8: 779\u2013790.","journal-title":"Genome Res"},{"issue":"1\u20132","key":"2529_CR8","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1023\/A:1003705601428","volume":"106","author":"MY Galperin","year":"1999","unstructured":"Galperin MY, Koonin EV: Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes. Genetica 1999, 106(1\u20132):159\u2013170.","journal-title":"Genetica"},{"issue":"7","key":"2529_CR9","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1038\/nbt834","volume":"21","author":"E Morett","year":"2003","unstructured":"Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P: Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol 2003, 21(7):790\u2013795.","journal-title":"Nat Biotechnol"},{"issue":"5733","key":"2529_CR10","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1126\/science.1112642","volume":"309","author":"M Berriman","year":"2005","unstructured":"Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, B? U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UCM, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Aavies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DMA, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CMR, Tait A, Tivey AR, Aken SV, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM: The Genome of the African Trypanosome Trypanosoma brucei . Science 2005, 309(5733):416\u2013422.","journal-title":"Science"},{"key":"2529_CR11","doi-asserted-by":"publisher","first-page":"D354","DOI":"10.1093\/nar\/gkj102","volume":"34","author":"M Kanehisa","year":"2006","unstructured":"Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34: D354-D357.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"2529_CR12","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1016\/S0167-7799(99)01316-5","volume":"17","author":"PD Karp","year":"1999","unstructured":"Karp PD: Integrated pathway\/genome databases and their role in drug discovery. Trends in Biotechnology 1999, 17(7):275\u2013281.","journal-title":"Trends in Biotechnology"},{"key":"2529_CR13","unstructured":"Kegg ftp download[ ftp:\/\/ftp.genome.ad.jp\/pub\/kegg\/ ]"},{"key":"2529_CR14","volume-title":"The Design and Analysis of Computer Algorithms. Addison-Wesley","author":"AV Aho","year":"1974","unstructured":"Aho AV, Hopcroft JE, Ullman JD: The Design and Analysis of Computer Algorithms. Addison-Wesley. 1974."},{"key":"2529_CR15","volume-title":"Introduction to Algorithms","author":"TT Cormen","year":"2001","unstructured":"Cormen TT, Leiserson CE, Rivest RL: Introduction to Algorithms. 2nd edition. Mit Press; 2001.","edition":"2"},{"key":"2529_CR16","unstructured":"Color Objects in KEGG Pathways[ http:\/\/www.genome.jp\/kegg\/tool\/color_pathway.html ]"},{"issue":"22","key":"2529_CR17","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: Clustal W: improving the sensitivity of progressive Multiple sequence alignment through sequence weighting, position-specific gap penalties and Weight matrix choice. Nucleic Acids Res 1994, 22(22):4673\u20134680.","journal-title":"Nucleic Acids Res"},{"issue":"5733","key":"2529_CR18","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1126\/science.1112680","volume":"309","author":"AC Ivens","year":"2005","unstructured":"Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RMR, Cronin A, Cruz AK, Davies RM, Gaudenzi JD, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Boffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, Muller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Schr M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ: The genome of the Kinetoplastid parasite, Leishmania major . Science 2005, 309(5733):436\u2013342.","journal-title":"Science"},{"issue":"8","key":"2529_CR19","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1186\/gb-2004-5-8-401","volume":"5","author":"PD Karp","year":"2004","unstructured":"Karp PD: Call for an enzyme genomics initiative. Genome Biol 2004, 5(8):401.","journal-title":"Genome Biol"},{"key":"2529_CR20","doi-asserted-by":"publisher","first-page":"W182","DOI":"10.1093\/nar\/gkm321","volume":"35","author":"Y Moriya","year":"2007","unstructured":"Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M: KAAS: an automatic genome annotation and Pathway reconstruction server. Nucleic Acids Res 2007, 35: W182-W185.","journal-title":"Nucleic Acids Res"},{"key":"2529_CR21","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1093\/nar\/gkl167","volume":"1","author":"J Wu","year":"2006","unstructured":"Wu J, Mao X, Cai T, Luo J, Wei L: KOBAS server: a web-based platform for automated annotation And pathway identification. Nucleic Acids Res 2006, 1: 720\u2013724.","journal-title":"Nucleic Acids Res"},{"key":"2529_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S1387-2656(05)11001-1","volume":"11","author":"HP Fischer","year":"2005","unstructured":"Fischer HP: Towards quantitative biology: Integration of biological information to elucidate Disease pathways and to guide drug discovery. Biotechnology Annual Review 2005, 11: 1\u201368.","journal-title":"Biotechnology Annual Review"},{"issue":"7","key":"2529_CR23","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/35080529","volume":"2","author":"L Stein","year":"2001","unstructured":"Stein L: Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2(7):493\u2013503.","journal-title":"Nat Rev Genet"},{"key":"2529_CR24","first-page":"365","volume":"13","author":"E Morett","year":"2002","unstructured":"Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P: Discovery of Analogous Enzymes in Thiamin Biosynthesis by Anticorrelation. Genome Informatics 2002, 13: 365\u2013366.","journal-title":"Genome Informatics"},{"issue":"5733","key":"2529_CR25","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1126\/science.1112181","volume":"309","author":"NM El-Sayed","year":"2005","unstructured":"El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UCM, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N: Comparative Genomics of Trypanosomatid Parasitic Protozoa. Science 2005, 309(5733):404\u2013409.","journal-title":"Science"},{"issue":"2","key":"2529_CR26","first-page":"286","volume":"1","author":"TD Otto","year":"2007","unstructured":"Otto TD, Catanho M, Degrave W, de Miranda AB: The PDTIS bioinformatics platform: from sequence to function. RECIIs 2007, 1(2):286\u2013294.","journal-title":"RECIIs"},{"issue":"1","key":"2529_CR27","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1128\/IAI.59.1.7-17.1991","volume":"59","author":"JV Gilbert","year":"1991","unstructured":"Gilbert JV, Plaut AG, Wright A: Analysis of the immunoglobulin A protease gene of Streptococcus sanguis. Infect Immun 1991, 59(1):7\u201317.","journal-title":"Infect Immun"},{"issue":"17","key":"2529_CR28","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1073\/pnas.1733211100","volume":"100","author":"A Dufresne","year":"2003","unstructured":"Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Gall FL, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, de Marsac NT, Weissenbach J, Wincker P, Wolf YI, Hess WR: Genome sequence of the cyanobacterium Prochlorococcus marinus ss120, a nearly minimal oxyphototrophic genome. PNAS 2003, 100(17):7\u201317.","journal-title":"PNAS"},{"key":"2529_CR29","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1039\/cs9972600337","volume":"26","author":"KA Reynolds","year":"1997","unstructured":"Reynolds KA, Holland KA: The mechanistic and evolutionary basis of stereospecificity for hydrogen Transfers in enzyme-catalysed processes. Chemical Society Reviews 1997, 26: 337\u2013343.","journal-title":"Chemical Society Reviews"},{"issue":"5","key":"2529_CR30","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1128\/AEM.62.5.1728-1740.1996","volume":"62","author":"JJ Kukor","year":"1996","unstructured":"Kukor JJ, Olsen RH: Catechol 2,3-dioxygenases functional in oxygen-limited (hypoxic) environments. Appl Environ Microbiol 1996, 62(5):583\u2013585.","journal-title":"Appl Environ Microbiol"},{"key":"2529_CR31","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1104\/pp.45.5.583","volume":"45","author":"LE Anderson","year":"1970","unstructured":"Anderson LE, Pacold I: Chloroplast and Cytoplasmic Enzymes: Three Distinct Isoenzymes Associated with the Reductive Pentose Phosphate Cycle. Plant Physiology 1970, 45: 583\u2013585.","journal-title":"Plant Physiology"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-544.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-544\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-544.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,13]],"date-time":"2020-05-13T22:09:05Z","timestamp":1589407745000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-544"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,12]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2529"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-544","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,12]]},"article-number":"544"}}