{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T16:06:08Z","timestamp":1783008368597,"version":"3.54.5"},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Polyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common \u03b1\/\u03b2-hydrolase fold and a catalytic triad, which is also found in other \u03b1\/\u03b2-hydrolases.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The PHA Depolymerase Engineering Database (DED, <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.ded.uni-stuttgart.de\" ext-link-type=\"uri\">http:\/\/www.ded.uni-stuttgart.de<\/jats:ext-link>) has been established as a tool for systematic analysis of this enzyme family. The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity. For each family, multiple sequence alignments and profile hidden Markov models are provided, and functionally relevant residues are annotated.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes <jats:italic>in silico<\/jats:italic>, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-89","type":"journal-article","created":{"date-parts":[[2009,3,19]],"date-time":"2009-03-19T07:13:14Z","timestamp":1237446794000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":142,"title":["The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases"],"prefix":"10.1186","volume":"10","author":[{"given":"Michael","family":"Knoll","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas M","family":"Hamm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginia","family":"Martinez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00fcrgen","family":"Pleiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2009,3,18]]},"reference":[{"issue":"4","key":"2819_CR1","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1128\/mr.54.4.450-472.1990","volume":"54","author":"AJ Anderson","year":"1990","unstructured":"Anderson AJ, Dawes EA: Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev 1990, 54(4):450\u2013472.","journal-title":"Microbiol Rev"},{"issue":"2","key":"2819_CR2","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1128\/JB.01576-06","volume":"189","author":"MA Prieto","year":"2007","unstructured":"Prieto MA: From oil to bioplastics, a dream come true? Journal of Bacteriology 2007, 189(2):289\u2013290. 10.1128\/JB.01576-06","journal-title":"Journal of Bacteriology"},{"issue":"41","key":"2819_CR3","doi-asserted-by":"publisher","first-page":"29228","DOI":"10.1074\/jbc.274.41.29228","volume":"274","author":"B Garcia","year":"1999","unstructured":"Garcia B, Olivera ER, Minambres B, Fernandez-Valverde M, Canedo LM, Prieto MA, Garcia JL, Martinez M, Luengo JM: Novel biodegradable aromatic plastics from a bacterial source \u2013 Genetic and biochemical studies on a route of the phenylacetyl-CoA catabolon. Journal of Biological Chemistry 1999, 274(41):29228\u201329241. 10.1074\/jbc.274.41.29228","journal-title":"Journal of Biological Chemistry"},{"issue":"15","key":"2819_CR4","doi-asserted-by":"publisher","first-page":"1181","DOI":"10.1023\/B:BILE.0000036599.15302.e5","volume":"26","author":"Y Tokiwa","year":"2004","unstructured":"Tokiwa Y, Calabia BP: Degradation of microbial polyesters. Biotechnol Lett 2004, 26(15):1181\u20131189. 10.1023\/B:BILE.0000036599.15302.e5","journal-title":"Biotechnol Lett"},{"key":"2819_CR5","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1146\/annurev.micro.56.012302.160838","volume":"56","author":"D Jendrossek","year":"2002","unstructured":"Jendrossek D, Handrick R: Microbial degradation of polyhydroxyalkanoates. Annu Rev Microbiol 2002, 56: 403\u2013432. 10.1146\/annurev.micro.56.012302.160838","journal-title":"Annu Rev Microbiol"},{"issue":"39","key":"2819_CR6","doi-asserted-by":"publisher","first-page":"36215","DOI":"10.1074\/jbc.M101106200","volume":"276","author":"R Handrick","year":"2001","unstructured":"Handrick R, Reinhardt S, Focarete ML, Scandola M, Adamus G, Kowalczuk M, Jendrossek D: A new type of thermoalkalophilic hydrolase of Paucimonas lemoignei with high specificity for amorphous polyesters of short chain-length hydroxyalkanoic acids. J Biol Chem 2001, 276(39):36215\u201336224. 10.1074\/jbc.M101106200","journal-title":"J Biol Chem"},{"issue":"21","key":"2819_CR7","doi-asserted-by":"publisher","first-page":"7243","DOI":"10.1128\/JB.186.21.7243-7253.2004","volume":"186","author":"R Handrick","year":"2004","unstructured":"Handrick R, Reinhardt S, Kimmig P, Jendrossek D: The \"intracellular\" poly(3-hydroxybutyrate) (PHB) depolymerase of Rhodospirillum rubrum is a periplasm-located protein with specificity for native PHB and with structural similarity to extracellular PHB depolymerases. J Bacteriol 2004, 186(21):7243\u20137253. 10.1128\/JB.186.21.7243-7253.2004","journal-title":"J Bacteriol"},{"key":"2819_CR8","first-page":"D281","volume-title":"Nucleic Acids Res","author":"RD Finn","year":"2008","unstructured":"Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, et al.: The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281\u2013288."},{"issue":"8","key":"2819_CR9","doi-asserted-by":"crossref","first-page":"3113","DOI":"10.1128\/aem.61.8.3113-3118.1995","volume":"61","author":"KE Jaeger","year":"1995","unstructured":"Jaeger KE, Steinb\u00fcchel A, Jendrossek D: Substrate specificities of bacterial polyhydroxyalkanoate depolymerases and lipases: bacterial lipases hydrolyze poly(omega-hydroxyalkanoates). Appl Environ Microbiol 1995, 61(8):3113\u20133118.","journal-title":"Appl Environ Microbiol"},{"issue":"2\u20133","key":"2819_CR10","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1111\/j.1574-6968.1996.tb08479.x","volume":"143","author":"A Behrends","year":"1996","unstructured":"Behrends A, Klingbeil B, Jendrossek D: Poly(3-hydroxybutyrate) depolymerases bind to their substrate by a C-terminal located substrate binding site. Fems Microbiol Lett 1996, 143(2\u20133):191\u2013194. 10.1111\/j.1574-6968.1996.tb08479.x","journal-title":"Fems Microbiol Lett"},{"issue":"20","key":"2819_CR11","doi-asserted-by":"publisher","first-page":"5916","DOI":"10.1128\/JB.182.20.5916-5918.2000","volume":"182","author":"R Handrick","year":"2000","unstructured":"Handrick R, Reinhardt S, Jendrossek D: Mobilization of poly(3-hydroxybutyrate) in Ralstonia eutropha. J Bacteriol 2000, 182(20):5916\u20135918. 10.1128\/JB.182.20.5916-5918.2000","journal-title":"J Bacteriol"},{"issue":"5","key":"2819_CR12","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/S1381-1177(00)00092-8","volume":"10","author":"J Pleiss","year":"2000","unstructured":"Pleiss J, Fischer M, Peiker M, Thiele C, Schmid RD: Lipase engineering database \u2013 Understanding and exploiting sequence-structure-function relationships. J Mol Catal B-Enzym 2000, 10(5):491\u2013508. 10.1016\/S1381-1177(00)00092-8","journal-title":"J Mol Catal B-Enzym"},{"issue":"1","key":"2819_CR13","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1093\/nar\/gkg015","volume":"31","author":"M Fischer","year":"2003","unstructured":"Fischer M, Pleiss J: The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Research 2003, 31(1):319\u2013321. 10.1093\/nar\/gkg015","journal-title":"Nucleic Acids Research"},{"key":"2819_CR14","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1186\/1471-2105-7-495","volume":"7","author":"M Fischer","year":"2006","unstructured":"Fischer M, Thai QK, Grieb M, Pleiss J: DWARF \u2013 a data warehouse system for analyzing protein families. BMC Bioinformatics 2006, 7: 495. 10.1186\/1471-2105-7-495","journal-title":"BMC Bioinformatics"},{"key":"2819_CR15","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1007\/BF02074776","volume":"2","author":"BH Briese","year":"1994","unstructured":"Briese BH, Schmidt B, Jendrossek D: Pseudomonas lemoignei has five poly(hydroxyalkanoic acid) (PHA) depolymerase genes: a comparative study of bacterial and eucaryotic PHA depolymerases. J Environ Polym Degrad 1994, 2: 75\u201387. 10.1007\/BF02074776","journal-title":"J Environ Polym Degrad"},{"issue":"2","key":"2819_CR16","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/0003-9861(91)90572-Z","volume":"290","author":"CL Brucato","year":"1991","unstructured":"Brucato CL, Wong SS: Extracellular poly(3-hydroxybutyrate) depolymerase from Penicillium funiculosum: general characteristics and active site studies. Arch Biochem Biophys 1991, 290(2):497\u2013502. 10.1016\/0003-9861(91)90572-Z","journal-title":"Arch Biochem Biophys"},{"issue":"7","key":"2819_CR17","doi-asserted-by":"publisher","first-page":"4951","DOI":"10.1074\/jbc.M608119200","volume":"282","author":"LI de Eugenio","year":"2007","unstructured":"de Eugenio LI, Garcia P, Luengo JM, Sanz JM, Roman JS, Garcia JL, Prieto MA: Biochemical evidence that phaZ gene encodes a specific intracellular medium chain length polyhydroxyalkanoate depolymerase in Pseudomonas putida KT2442: characterization of a paradigmatic enzyme. J Biol Chem 2007, 282(7):4951\u20134962. 10.1074\/jbc.M608119200","journal-title":"J Biol Chem"},{"issue":"4","key":"2819_CR18","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1016\/S0021-9258(18)52227-4","volume":"266","author":"GW Huisman","year":"1991","unstructured":"Huisman GW, Wonink E, Meima R, Kazemier B, Terpstra P, Witholt B: Metabolism of poly(3-hydroxyalkanoates) (PHAs) by Pseudomonas oleovorans. Identification and sequences of genes and function of the encoded proteins in the synthesis and degradation of PHA. J Biol Chem 1991, 266(4):2191\u20132198.","journal-title":"J Biol Chem"},{"key":"2819_CR19","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1139\/m95-183","volume":"41","author":"D Jendrossek","year":"1995","unstructured":"Jendrossek D, Backhaus M, Andermann M: Characterization of the Extracellular Poly(3-Hydroxybutyrate) Depolymerase of Comamonas Sp and of Its Structural Gene. Can J Microbiol 1995, 41: 160\u2013169.","journal-title":"Can J Microbiol"},{"issue":"2","key":"2819_CR20","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1111\/j.1432-1033.1993.tb18424.x","volume":"218","author":"D Jendrossek","year":"1993","unstructured":"Jendrossek D, Muller B, Schlegel HG: Cloning and characterization of the poly(hydroxyalkanoic acid)-depolymerase gene locus, phaZ1, of Pseudomonas lemoignei and its gene product. Eur J Biochem 1993, 218(2):701\u2013710. 10.1111\/j.1432-1033.1993.tb18424.x","journal-title":"Eur J Biochem"},{"issue":"12","key":"2819_CR21","doi-asserted-by":"crossref","first-page":"4844","DOI":"10.1128\/aem.63.12.4844-4852.1997","volume":"63","author":"KI Kasuya","year":"1609","unstructured":"Kasuya KI, Inoue Y, Tanaka T, Akehata T, Iwata T, Fukui T, Doi Y: Biochemical and molecular characterization of the polyhydroxybutyrate depolymerase of Comamonas acidovorans YM isolated from freshwater. Appl Environ Microb 1609, 63(12):4844\u20134852.","journal-title":"Appl Environ Microb"},{"issue":"3","key":"2819_CR22","first-page":"285","volume":"43","author":"DY Kim","year":"2005","unstructured":"Kim DY, Kim HC, Kim SY, Rhee YH: Molecular characterization of extracellular medium-chain-length poly(3-hydroxyalkanoate) depolymerase genes from Pseudomonas alcaligenes strains. J Microbiol 2005, 43(3):285\u2013294.","journal-title":"J Microbiol"},{"issue":"1","key":"2819_CR23","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/S0167-4781(97)00011-0","volume":"1352","author":"K Kita","year":"1997","unstructured":"Kita K, Mashiba S, Nagita M, Ishimaru K, Okamoto K, Yanase H, Kato N: Cloning of poly(3-hydroxybutyrate) depolymerase from a marine bacterium, Alcaligenes faecalis AE122, and characterization of its gene product. Biochim Biophys Acta 1997, 1352(1):113\u2013122.","journal-title":"Biochim Biophys Acta"},{"issue":"2\u20133","key":"2819_CR24","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1111\/j.1574-6968.1996.tb08433.x","volume":"142","author":"B Klingbeil","year":"1996","unstructured":"Klingbeil B, Kroppenstedt RM, Jendrossek D: Taxonomic identification of Streptomyces exfoliatus K10 and characterization of its poly(3-hydroxybutyrate) depolymerase gene. Fems Microbiol Lett 1996, 142(2\u20133):215\u2013221. 10.1111\/j.1574-6968.1996.tb08433.x","journal-title":"Fems Microbiol Lett"},{"issue":"1","key":"2819_CR25","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1023\/A:1021885901119","volume":"7","author":"T Kobayashi","year":"1999","unstructured":"Kobayashi T, Sugiyama A, Kawase Y, Saito T, Mergaert J, Swings J: Biochemical and genetic characterization of an extracellular poly(3-hydroxybutyrate) depolymerase from Acidovorax sp strain TP4. J Environ Polym Degr 1999, 7(1):9\u201318. 10.1023\/A:1021885901119","journal-title":"J Environ Polym Degr"},{"issue":"1","key":"2819_CR26","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1128\/AEM.65.1.189-197.1999","volume":"65","author":"T Ohura","year":"1999","unstructured":"Ohura T, Kasuya KI, Doi Y: Cloning and characterization of the polyhydroxybutyrate depolymerase gene of Pseudomonas stutzeri and analysis of the function of substrate-binding domains. Appl Environ Microbiol 1999, 65(1):189\u2013197.","journal-title":"Appl Environ Microbiol"},{"issue":"2\u20133","key":"2819_CR27","first-page":"157","volume":"182","author":"F Romen","year":"2004","unstructured":"Romen F, Reinhardt S, Jendrossek D: Thermotolerant poly(3-hydroxybutyrate)-degrading bacteria from hot compost and characterization of the PHB depolymerase of Schlegelella sp KB1a. Arch Microbiol 2004, 182(2\u20133):157\u2013164.","journal-title":"Arch Microbiol"},{"issue":"1","key":"2819_CR28","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1128\/JB.183.1.94-100.2001","volume":"183","author":"H Saegusa","year":"2001","unstructured":"Saegusa H, Shiraki M, Kanai C, Saito T: Cloning of an intracellular Poly[D(-)-3-Hydroxybutyrate] depolymerase gene from Ralstonia eutropha H16 and characterization of the gene product. J Bacteriol 2001, 183(1):94\u2013100. 10.1128\/JB.183.1.94-100.2001","journal-title":"J Bacteriol"},{"issue":"1","key":"2819_CR29","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1128\/jb.171.1.184-189.1989","volume":"171","author":"T Saito","year":"1989","unstructured":"Saito T, Suzuki K, Yamamoto J, Fukui T, Miwa K, Tomita K, Nakanishi S, Odani S, Suzuki J, Ishikawa K: Cloning, nucleotide sequence, and expression in Escherichia coli of the gene for poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis. J Bacteriol 1989, 171(1):184\u2013189.","journal-title":"J Bacteriol"},{"issue":"22","key":"2819_CR30","doi-asserted-by":"crossref","first-page":"7065","DOI":"10.1128\/jb.176.22.7065-7073.1994","volume":"176","author":"A Schirmer","year":"1994","unstructured":"Schirmer A, Jendrossek D: Molecular characterization of the extracellular poly(3-hydroxyoctanoic acid) [P(3HO)] depolymerase gene of Pseudomonas fluorescens GK13 and of its gene product. J Bacteriol 1994, 176(22):7065\u20137073.","journal-title":"J Bacteriol"},{"issue":"4","key":"2819_CR31","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1128\/AEM.66.4.1385-1392.2000","volume":"66","author":"U Schober","year":"2000","unstructured":"Schober U, Thiel C, Jendrossek D: Poly(3-hydroxyvalerate) depolymerase of Pseudomonas lemoignei. Appl Environ Microbiol 2000, 66(4):1385\u20131392. 10.1128\/AEM.66.4.1385-1392.2000","journal-title":"Appl Environ Microbiol"},{"issue":"2","key":"2819_CR32","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1111\/j.1574-6968.2006.00448.x","volume":"264","author":"H Takaku","year":"2006","unstructured":"Takaku H, Kimoto A, Kodaira S, Nashimoto M, Takagi M: Isolation of a Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterium from compost, and cloning and characterization of a gene encoding PHB depolymerase of Bacillus megaterium N-18\u201325\u20139. Fems Microbiology Letters 2006, 264(2):152\u2013159. 10.1111\/j.1574-6968.2006.00448.x","journal-title":"Fems Microbiology Letters"},{"issue":"4","key":"2819_CR33","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1016\/S1389-1723(01)80011-6","volume":"90","author":"M Takeda","year":"2000","unstructured":"Takeda M, Kitashima K, Adachi K, Hanaoka Y, Suzuki I, Koizumi JI: Cloning and expression of the gene encoding thermostable poly(3-hydroxybutyrate) depolymerase. J Biosci Bioeng 2000, 90(4):416\u2013421.","journal-title":"J Biosci Bioeng"},{"key":"2819_CR34","volume-title":"BIOspektrum","author":"D Jendrossek","year":"2001","unstructured":"Jendrossek D, Handrick R: Diversit\u00e4t bakterieller PHB-Depolymerasen am Beispiel von Paucimonas gen. nov. lemoignei comb. nov. BIOspektrum 2001., 7:"},{"issue":"21","key":"2819_CR35","doi-asserted-by":"publisher","first-page":"7592","DOI":"10.1128\/JB.00729-06","volume":"188","author":"CL Tseng","year":"2006","unstructured":"Tseng CL, Chen HJ, Shaw GC: Identification and characterization of the Bacillus thuringiensis phaZ gene, encoding new intracellular poly-3-hydroxybutyrate depolymerase. J Bacteriol 2006, 188(21):7592\u20137599. 10.1128\/JB.00729-06","journal-title":"J Bacteriol"},{"key":"2819_CR36","doi-asserted-by":"crossref","unstructured":"Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Res 2007, (35 Database):D21\u201325. 10.1093\/nar\/gkl986","DOI":"10.1093\/nar\/gkl986"},{"issue":"17","key":"2819_CR37","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(17):3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2819_CR38","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28(1):235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"2819_CR39","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577\u20132637. 10.1002\/bip.360221211","journal-title":"Biopolymers"},{"issue":"22","key":"2819_CR40","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. 10.1093\/nar\/22.22.4673","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"2819_CR41","doi-asserted-by":"publisher","first-page":"6982","DOI":"10.1128\/JB.187.20.6982-6990.2005","volume":"187","author":"T Abe","year":"2005","unstructured":"Abe T, Kobayashi T, Saito T: Properties of a novel intracellular poly(3-hydroxybutyrate) depolymerase with high specific activity (PhaZd) in Wautersia eutropha H16. Journal of Bacteriology 2005, 187(20):6982\u20136990. 10.1128\/JB.187.20.6982-6990.2005","journal-title":"Journal of Bacteriology"},{"issue":"15","key":"2819_CR42","doi-asserted-by":"publisher","first-page":"2015","DOI":"10.1093\/bioinformatics\/btm268","volume":"23","author":"M Fischer","year":"2007","unstructured":"Fischer M, Knoll M, Sirim D, Wagner F, Funke S, Pleiss J: The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family. Bioinformatics 2007, 23(15):2015\u20132017. 10.1093\/bioinformatics\/btm268","journal-title":"Bioinformatics"},{"key":"2819_CR43","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.1110\/ps.035428.108","volume":"17","author":"M Knoll","year":"2008","unstructured":"Knoll M, Pleiss J: The Medium-Chain Dehydrogenase\/Reductase Engineering Database: A systematic analysis of a diverse protein family to understand sequence-structure-function relationship. Protein Sci 2008, 17: 1689\u20131697. 10.1110\/ps.035428.108","journal-title":"Protein Sci"},{"issue":"6","key":"2819_CR44","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276\u2013277. 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends Genet"},{"issue":"3","key":"2819_CR45","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1128\/jb.177.3.596-607.1995","volume":"177","author":"D Jendrossek","year":"1995","unstructured":"Jendrossek D, Frisse A, Behrends A, Andermann M, Kratzin HD, Stanislawski T, Schlegel HG: Biochemical and molecular characterization of the Pseudomonas lemoignei polyhydroxyalkanoate depolymerase system. J Bacteriol 1995, 177(3):596\u2013607.","journal-title":"J Bacteriol"},{"issue":"4","key":"2819_CR46","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1016\/j.jmb.2005.12.028","volume":"356","author":"T Hisano","year":"2006","unstructured":"Hisano T, Kasuya K, Tezuka Y, Ishii N, Kobayashi T, Shiraki M, Oroudjev E, Hansma H, Iwata T, Doi Y, et al.: The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters. J Mol Biol 2006, 356(4):993\u20131004. 10.1016\/j.jmb.2005.12.028","journal-title":"J Mol Biol"},{"issue":"5","key":"2819_CR47","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1016\/j.jmb.2008.07.078","volume":"382","author":"AC Papageorgiou","year":"2008","unstructured":"Papageorgiou AC, Hermawan S, Singh CB, Jendrossek D: Structural basis of poly(3-hydroxybutyrate) hydrolysis by PhaZ7 depolymerase from Paucimonas lemoignei. J Mol Biol 2008, 382(5):1184\u20131194. 10.1016\/j.jmb.2008.07.078","journal-title":"J Mol Biol"},{"issue":"2","key":"2819_CR48","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1111\/j.1574-6968.2006.00448.x","volume":"264","author":"H Takaku","year":"2006","unstructured":"Takaku H, Kimoto A, Kodaira S, Nashimoto M, Takagi M: Isolation of a Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterium from compost, and cloning and characterization of a gene encoding PHB depolymerase of Bacillus megaterium N-18\u201325\u20139. Fems Microbiol Lett 2006, 264(2):152\u2013159. 10.1111\/j.1574-6968.2006.00448.x","journal-title":"Fems Microbiol Lett"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-89.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:42:24Z","timestamp":1630446144000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-89"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,3,18]]},"references-count":48,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2819"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-89","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,3,18]]},"assertion":[{"value":"28 November 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 March 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 March 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"89"}}