{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T02:06:03Z","timestamp":1780538763848,"version":"3.54.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2016,11,9]],"date-time":"2016-11-09T00:00:00Z","timestamp":1478649600000},"content-version":"vor","delay-in-days":744,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,28]]},"DOI":"10.1093\/nar\/gku1002","type":"journal-article","created":{"date-parts":[[2014,10,28]],"date-time":"2014-10-28T00:15:12Z","timestamp":1414455312000},"page":"D1064-D1070","source":"Crossref","is-referenced-by-count":155,"title":["HAMAP in 2015: updates to the protein family classification and annotation system"],"prefix":"10.1093","volume":"43","author":[{"given":"Ivo","family":"Pedruzzi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Rivoire","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea H.","family":"Auchincloss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Coudert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillaume","family":"Keller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edouard","family":"de\u00a0Castro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Delphine","family":"Baratin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B\u00e9atrice A.","family":"Cuche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lydie","family":"Bougueleret","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Poux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Redaschi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Bridge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,10,27]]},"reference":[{"key":"key\n\t\t\t\t20171011194024_B1","doi-asserted-by":"crossref","first-page":"9950","DOI":"10.1021\/bi201312u","article-title":"Enzyme Function Initiative","volume":"50","author":"Gerlt","year":"2011","journal-title":"Biochemistry"},{"key":"key\n\t\t\t\t20171011194024_B2","doi-asserted-by":"crossref","first-page":"e1001638","DOI":"10.1371\/journal.pbio.1001638","article-title":"The COMBREX project: design, methodology, and initial results","volume":"11","author":"Anton","year":"2013","journal-title":"PLoS Biol."},{"key":"key\n\t\t\t\t20171011194024_B3","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/nmeth.2340","article-title":"A large-scale evaluation of computational protein function prediction","volume":"10","author":"Radivojac","year":"2013","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20171011194024_B4","doi-asserted-by":"crossref","first-page":"D584","DOI":"10.1093\/nar\/gks1157","article-title":"HAMAP in 2013, new developments in the protein family classification and annotation system","volume":"41","author":"Pedruzzi","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011194024_B5","doi-asserted-by":"crossref","first-page":"D530","DOI":"10.1093\/nar\/gks1050","article-title":"Gene Ontology annotations and resources","volume":"41","author":"Blake","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011194024_B6","doi-asserted-by":"crossref","first-page":"e1000605","DOI":"10.1371\/journal.pcbi.1000605","article-title":"Annotation error in public databases: misannotation of molecular function in enzyme superfamilies","volume":"5","author":"Schnoes","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20171011194024_B7","doi-asserted-by":"crossref","first-page":"e75541","DOI":"10.1371\/journal.pone.0075541","article-title":"Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB","volume":"8","author":"Bell","year":"2013","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20171011194024_B8","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/bioinformatics\/18.12.1641","article-title":"Modeling the percolation of annotation errors in a database of protein sequences","volume":"18","author":"Gilks","year":"2002","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011194024_B9","article-title":"UniProt: a hub for protein information","author":"UniProt Consortium","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011194024_B10","doi-asserted-by":"crossref","first-page":"D546","DOI":"10.1093\/nar\/gkt979","article-title":"Ensembl Genomes 2013: scaling up access to genome-wide data","volume":"42","author":"Kersey","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011194024_B11","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1186\/1471-2164-14-761","article-title":"Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads","volume":"14","author":"Darrasse","year":"2013","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20171011194024_B12","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1093\/gbe\/evt210","article-title":"Genome degeneration and adaptation in a nascent stage of symbiosis","volume":"6","author":"Oakeson","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"key\n\t\t\t\t20171011194024_B13","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/S1476-9271(02)00094-4","article-title":"Automated annotation of microbial proteomes in SWISS-PROT","volume":"27","author":"Gattiker","year":"2003","journal-title":"Comput. Biol. Chem."},{"key":"key\n\t\t\t\t20171011194024_B14","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0097-8485(96)80003-9","article-title":"A flexible motif search technique based on generalized profiles","volume":"20","author":"Bucher","year":"1996","journal-title":"Comput. Chem."},{"key":"key\n\t\t\t\t20171011194024_B15","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1093\/bib\/3.3.265","article-title":"PROSITE: a documented database using patterns and profiles as motif descriptors","volume":"3","author":"Sigrist","year":"2002","journal-title":"Brief Bioinform."},{"key":"key\n\t\t\t\t20171011194024_B16","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/pro.5560030118","article-title":"Improving the sensitivity of the sequence profile method","volume":"3","author":"Luthy","year":"1994","journal-title":"Protein Sci."},{"key":"key\n\t\t\t\t20171011194024_B17","first-page":"345","volume-title":"Atlas of protein sequence and structure","author":"Dayhoff","year":"1978"},{"key":"key\n\t\t\t\t20171011194024_B18","doi-asserted-by":"crossref","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","article-title":"Amino acid substitution matrices from protein blocks","volume":"89","author":"Henikoff","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"key\n\t\t\t\t20171011194024_B19","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1146\/annurev.biochem.74.082803.133500","article-title":"The biochemistry of sirtuins","volume":"75","author":"Sauve","year":"2006","journal-title":"Annu. Rev. Biochem."},{"key":"key\n\t\t\t\t20171011194024_B20","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/gb-2004-5-5-224","article-title":"Sirtuins: Sir2-related NAD-dependent protein deacetylases","volume":"5","author":"North","year":"2004","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171011194024_B21","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20171011194024_B22","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview version 2\u2013a multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011194024_B23","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1093\/bioinformatics\/btr088","article-title":"ProtTest 3: fast selection of best-fit models of protein evolution","volume":"27","author":"Darriba","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011194024_B24","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20171011194024_B25","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011194024_B26","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M111.012658","article-title":"The first identification of lysine malonylation substrates and its regulatory enzyme","volume":"10","author":"Peng","year":"2011","journal-title":"Mol. Cell. Proteomics"},{"key":"key\n\t\t\t\t20171011194024_B27","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1126\/science.1207861","article-title":"Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase","volume":"334","author":"Du","year":"2011","journal-title":"Science"},{"key":"key\n\t\t\t\t20171011194024_B28","doi-asserted-by":"crossref","first-page":"3509","DOI":"10.1074\/mcp.M113.031567","article-title":"Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli","volume":"12","author":"Colak","journal-title":"Mol. Cell. Proteomics"},{"key":"key\n\t\t\t\t20171011194024_B29","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1021\/cb200230x","article-title":"Plasmodium falciparum Sir2A preferentially hydrolyzes medium and long chain fatty acyl lysine","volume":"7","author":"Zhu","year":"2011","journal-title":"ACS Chem. Biol."},{"key":"key\n\t\t\t\t20171011194024_B30","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1006\/bbrc.2000.3000","article-title":"Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins","volume":"273","author":"Frye","year":"2000","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"key\n\t\t\t\t20171011194024_B31","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bau016","article-title":"Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data","author":"Poux","year":"2014","journal-title":"Database (Oxford)"},{"key":"key\n\t\t\t\t20171011194024_B32","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/S0378-1119(03)00797-2","article-title":"Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase","volume":"318","author":"Bapteste","year":"2003","journal-title":"Gene"},{"key":"key\n\t\t\t\t20171011194024_B33","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/S0969-2126(02)00760-8","article-title":"The structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi","volume":"10","author":"Moore","year":"2002","journal-title":"Structure"},{"key":"key\n\t\t\t\t20171011194024_B34","doi-asserted-by":"crossref","first-page":"35677","DOI":"10.1074\/jbc.C000581200","article-title":"The primordial high energy compound: ATP or inorganic pyrophosphate?","volume":"275","author":"Chi","year":"2000","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20171011194024_B35","doi-asserted-by":"crossref","first-page":"6714","DOI":"10.1128\/JB.183.22.6714-6716.2001","article-title":"Presence of prokaryotic and eukaryotic species in all subgroups of the PP(i)-dependent group II phosphofructokinase protein family","volume":"183","author":"Muller","year":"2001","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20171011194024_B36","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011194024_B37","doi-asserted-by":"crossref","first-page":"D306","DOI":"10.1093\/nar\/gkr948","article-title":"InterPro in 2011: new developments in the family and domain prediction database","volume":"40","author":"Hunter","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011194024_B38","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1093\/bioinformatics\/btt129","article-title":"pfsearchV3: a code acceleration and heuristic to search PROSITE profiles","volume":"29","author":"Schuepbach","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/43\/D1\/D1064\/17435805\/gku1002.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:41:42Z","timestamp":1522680102000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/43\/D1\/D1064\/2435286\/HAMAP-in-2015-updates-to-the-protein-family"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,27]]},"references-count":38,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2014,10,27]]},"published-print":{"date-parts":[[2015,1,28]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gku1002","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,28]]},"published":{"date-parts":[[2014,10,27]]}}}