{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T10:48:21Z","timestamp":1782211701502,"version":"3.54.5"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2017,10,27]],"date-time":"2017-10-27T00:00:00Z","timestamp":1509062400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,4]]},"DOI":"10.1093\/nar\/gkx1022","type":"journal-article","created":{"date-parts":[[2017,10,25]],"date-time":"2017-10-25T15:21:53Z","timestamp":1508944913000},"page":"D677-D683","source":"Crossref","is-referenced-by-count":264,"title":["PULDB: the expanded database of Polysaccharide Utilization Loci"],"prefix":"10.1093","volume":"46","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3693-6017","authenticated-orcid":false,"given":"Nicolas","family":"Terrapon","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Lombard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c9lodie","family":"Drula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascal","family":"Lap\u00e9bie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saad","family":"Al-Masaudi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harry J","family":"Gilbert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernard","family":"Henrissat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,10,27]]},"reference":[{"key":"key\n\t\t\t\t20180103185619_B1","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.chom.2008.09.007","article-title":"Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont","volume":"4","year":"2008","journal-title":"Cell Host Microbe"},{"key":"key\n\t\t\t\t20180103185619_B2","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nrmicro3050","article-title":"The abundance and variety of carbohydrate-active enzymes in the human gut microbiota","volume":"11","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"key\n\t\t\t\t20180103185619_B3","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1093\/bioinformatics\/btu716","article-title":"Automatic prediction of polysaccharide utilization loci in Bacteroidetes species","volume":"31","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180103185619_B4","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/bti123","article-title":"Operon prediction without a training set","volume":"21","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180103185619_B5","doi-asserted-by":"crossref","first-page":"D490","DOI":"10.1093\/nar\/gkt1178","article-title":"The carbohydrate-active enzymes database (CAZy) in 2013","volume":"42","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185619_B6","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1186\/1471-2105-12-385","article-title":"Interactive metagenomic visualization in a Web browser","volume":"12","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180103185619_B7","doi-asserted-by":"crossref","first-page":"e1001637","DOI":"10.1371\/journal.pbio.1001637","article-title":"Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome","volume":"11","year":"2013","journal-title":"PLoS Biol."},{"key":"key\n\t\t\t\t20180103185619_B8","doi-asserted-by":"crossref","first-page":"aac5992","DOI":"10.1126\/science.aac5992","article-title":"Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides","volume":"350","year":"2015","journal-title":"Science"},{"key":"key\n\t\t\t\t20180103185619_B9","doi-asserted-by":"crossref","first-page":"4610","DOI":"10.1111\/1462-2920.13584","article-title":"Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT","volume":"18","year":"2016","journal-title":"Environ. Microbiol."},{"key":"key\n\t\t\t\t20180103185619_B10","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1111\/j.1365-2958.2011.07750.x","article-title":"The genome and surface proteome of Capnocytophaga canimorsus reveal a key role of glycan foraging systems in host glycoproteins deglycosylation","volume":"81","year":"2011","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20180103185619_B11","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1016\/j.cell.2010.05.005","article-title":"Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations","volume":"141","year":"2010","journal-title":"Cell"},{"key":"key\n\t\t\t\t20180103185619_B12","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/s12864-016-2472-1","article-title":"Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis","volume":"17","year":"2016","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180103185619_B13","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1186\/s12864-016-2680-8","article-title":"Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level","volume":"17","year":"2016","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180103185619_B14","doi-asserted-by":"crossref","first-page":"7481","DOI":"10.1038\/ncomms8481","article-title":"Glycan complexity dictates microbial resource allocation in the large intestine","volume":"6","year":"2015","journal-title":"Nat. Commun."},{"key":"key\n\t\t\t\t20180103185619_B15","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1038\/nature12907","article-title":"A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes","volume":"506","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180103185619_B16","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/nature21725","article-title":"Complex pectin metabolism by gut bacteria reveals novel catalytic functions","volume":"544","year":"2017","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180103185619_B17","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/nature13995","article-title":"Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism","volume":"517","year":"2015","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180103185619_B18","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1074\/jbc.M116.746438","article-title":"Galactomannan catabolism conferred by a polysaccharide utilization locus of Bacteroides ovatus: ENZYME SYNERGY AND CRYSTAL STRUCTURE OF A beta-MANNANASE","volume":"292","year":"2017","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180103185619_B19","doi-asserted-by":"crossref","first-page":"10639","DOI":"10.1074\/jbc.M117.787606","article-title":"A Bacteroidetes locus dedicated to fungal 1,6-beta-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-beta-glucanase","volume":"292","year":"2017","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180103185619_B20","first-page":"e02507","article-title":"Glycan-foraging systems reveal the adaptation of Capnocytophaga canimorsus to the dog mouth","volume":"6","year":"2015","journal-title":"Mbio"},{"key":"key\n\t\t\t\t20180103185619_B21","doi-asserted-by":"crossref","first-page":"79","DOI":"10.2152\/jmi.59.79","article-title":"Characterization of a gene cluster for sialoglycoconjugate utilization in Bacteroides fragilis","volume":"59","year":"2012","journal-title":"J. Med. Invest."},{"key":"key\n\t\t\t\t20180103185619_B22","doi-asserted-by":"crossref","first-page":"e1002118","DOI":"10.1371\/journal.ppat.1002118","article-title":"The N-glycan glycoprotein deglycosylation complex (Gpd) from Capnocytophaga canimorsus deglycosylates human IgG","volume":"7","year":"2011","journal-title":"PLoS Pathog."},{"key":"key\n\t\t\t\t20180103185619_B23","doi-asserted-by":"crossref","first-page":"12901","DOI":"10.1073\/pnas.1407344111","article-title":"Efficient utilization of complex N-linked glycans is a selective advantage for Bacteroides fragilis in extraintestinal infections","volume":"111","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180103185619_B24","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/nature12447","article-title":"Bacterial colonization factors control specificity and stability of the gut microbiota","volume":"501","year":"2013","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180103185619_B25","doi-asserted-by":"crossref","first-page":"7037","DOI":"10.1073\/pnas.1704367114","article-title":"How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans","volume":"114","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180103185619_B26","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1186\/s13068-016-0674-z","article-title":"A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin","volume":"9","year":"2016","journal-title":"Biotechnol. Biofuels"},{"key":"key\n\t\t\t\t20180103185619_B27","doi-asserted-by":"crossref","first-page":"1492","DOI":"10.1038\/ismej.2014.4","article-title":"Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes \u2018Gramella forsetii\u2019 KT0803","volume":"8","year":"2014","journal-title":"ISME J."},{"key":"key\n\t\t\t\t20180103185619_B28","doi-asserted-by":"crossref","first-page":"25194","DOI":"10.1074\/jbc.M113.484733","article-title":"Lacto-N-biosidase encoded by a novel gene of Bifidobacterium longum subspecies longum shows unique substrate specificity and requires a designated chaperone for its active expression","volume":"288","year":"2013","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180103185619_B29","doi-asserted-by":"crossref","first-page":"7487","DOI":"10.1074\/jbc.M116.762724","article-title":"Biochemical and structural analyses of a bacterial endo-beta-1,2-glucanase reveal a new glycoside hydrolase family","volume":"292","year":"2017","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180103185619_B30","doi-asserted-by":"crossref","first-page":"4936","DOI":"10.1073\/pnas.1701130114","article-title":"Unusual active site location and catalytic apparatus in a glycoside hydrolase family","volume":"114","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180103185619_B31","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1021\/acschembio.7b00126","article-title":"New ulvan-degrading polysaccharide lyase family: structure and catalytic mechanism suggests convergent evolution of active site architecture","volume":"12","year":"2017","journal-title":"ACS Chem. Biol."},{"key":"key\n\t\t\t\t20180103185619_B32","doi-asserted-by":"crossref","first-page":"5871","DOI":"10.1074\/jbc.M115.673947","article-title":"New family of ulvan lyases identified in three isolates from the alteromonadales order","volume":"291","year":"2016","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180103185619_B33","doi-asserted-by":"crossref","first-page":"8515","DOI":"10.1007\/s00253-015-6600-7","article-title":"Molecular characterization of a Penicillium chrysogenum exo-rhamnogalacturonan lyase that is structurally distinct from other polysaccharide lyase family proteins","volume":"99","year":"2015","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"key\n\t\t\t\t20180103185619_B34","doi-asserted-by":"crossref","first-page":"13271","DOI":"10.1074\/jbc.M117.794578","article-title":"An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins","volume":"292","year":"2017","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180103185619_B35","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","year":"2009","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180103185619_B36","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: towards a more sustainable future","volume":"44","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185619_B37","first-page":"6","article-title":"Marine polysaccharide sulfatases","volume":"4","year":"2017","journal-title":"Front. Mar. Sci."},{"key":"key\n\t\t\t\t20180103185619_B38","doi-asserted-by":"crossref","first-page":"25973","DOI":"10.1074\/jbc.M111.228841","article-title":"Sulfatases and a radical S-adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont, Bacteroides thetaiotaomicron","volume":"286","year":"2011","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180103185619_B39","doi-asserted-by":"crossref","first-page":"e0164846","DOI":"10.1371\/journal.pone.0164846","article-title":"Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity","volume":"11","year":"2016","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180103185619_B40","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1146\/annurev-biophys-060414-033901","article-title":"Structural biology of the major facilitator superfamily transporters","volume":"44","year":"2015","journal-title":"Annu. Rev. Biophys."},{"key":"key\n\t\t\t\t20180103185619_B41","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1111\/mmi.13480","article-title":"Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli","volume":"102","year":"2016","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20180103185619_B42","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/j.2041-1014.2011.00630.x","article-title":"Sialic acid, periodontal pathogens and Tannerella forsythia: stick around and enjoy the feast!","volume":"27","year":"2012","journal-title":"Mol. Oral Microbiol."},{"key":"key\n\t\t\t\t20180103185619_B43","doi-asserted-by":"crossref","first-page":"3629","DOI":"10.1128\/JB.00811-08","article-title":"Sialic acid (N-acetyl neuraminic acid) utilization by Bacteroides fragilis requires a novel N-acetyl mannosamine epimerase","volume":"191","year":"2009","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20180103185619_B44","doi-asserted-by":"crossref","first-page":"D343","DOI":"10.1093\/nar\/gkv1118","article-title":"Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors","volume":"44","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185619_B45","doi-asserted-by":"crossref","first-page":"e1001221","DOI":"10.1371\/journal.pbio.1001221","article-title":"Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts","volume":"9","year":"2011","journal-title":"PLoS Biol."},{"key":"key\n\t\t\t\t20180103185619_B46","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1093\/bioinformatics\/btt379","article-title":"Rapid similarity search of proteins using alignments of domain arrangements","volume":"30","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180103185619_B47","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins","volume":"48","year":"1970","journal-title":"J. Mol. Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/D1\/D677\/23162027\/gkx1022.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:40:37Z","timestamp":1522665637000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/46\/D1\/D677\/4566598"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,27]]},"references-count":47,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2017,10,27]]},"published-print":{"date-parts":[[2018,1,4]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkx1022","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,1,4]]},"published":{"date-parts":[[2017,10,27]]}}}