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typhimurium<\/italic> Encodes Five Homologues of Carboxysome Shell Proteins","volume":"181","author":"E Kofoid","year":"1999","journal-title":"J Bacteriol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1128\/jb.177.5.1357-1366.1995","article-title":"Ethanolamine utilization in <italic>Salmonella typhimurium<\/italic>: nucleotide sequence, protein expression, and mutational analysis of the <italic>cchA cchB eutE eutJ eutG eutH<\/italic> gene cluster","volume":"177","author":"I Stojiljkovic","year":"1995","journal-title":"J Bacteriol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"5474","DOI":"10.1128\/jb.176.17.5474-5482.1994","article-title":"The control region of the <italic>pdu\/cob<\/italic> regulon in <italic>Salmonella typhimurium<\/italic>","volume":"176","author":"P Chen","year":"1994","journal-title":"J 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in the Metabolism of Fucose and Rhamnose by <italic>Clostridium phytofermentans<\/italic>","volume":"8","author":"E Petit","year":"2013","journal-title":"PLoS One"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2193","DOI":"10.1128\/AEM.03887-13","article-title":"Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides","volume":"80","author":"O Erbilgin","year":"2014","journal-title":"Appl Environ Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"10377","DOI":"10.1074\/jbc.M709285200","article-title":"CO2 fixation kinetics of <italic>Halothiobacillus neapolitanus<\/italic> mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for CO2","volume":"283","author":"Z Dou","year":"2008","journal-title":"J Biol Chem"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2966","DOI":"10.1128\/JB.01925-07","article-title":"Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate","volume":"190","author":"EM Sampson","year":"2008","journal-title":"J Bacteriol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1128\/JB.188.8.2865-2874.2006","article-title":"Conserving a Volatile Metabolite: a Role for Carboxysome-Like Organelles in <italic>Salmonella enterica<\/italic>","volume":"188","author":"JT Penrod","year":"2006","journal-title":"J Bacteriol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3855","DOI":"10.1128\/jb.170.9.3855-3863.1988","article-title":"Ethanolamine utilization in <italic>Salmonella typhimurium<\/italic>","volume":"170","author":"DM Roof","year":"1988","journal-title":"J Bacteriol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1007\/s00203-003-0601-0","article-title":"PduP is a coenzyme-a-acylating propionaldehyde dehydrogenase associated with the 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of <italic>Salmonella enterica<\/italic> Encodes a Protein with Phosphotransacetylase Enzyme Activity","volume":"186","author":"SR Brinsmade","year":"2004","journal-title":"J Bacteriol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1093\/genetics\/143.4.1843","article-title":"Selfish operons: horizontal transfer may drive the evolution of gene clusters","volume":"143","author":"JG Lawrence","year":"1996","journal-title":"Genetics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"14366","DOI":"10.1074\/jbc.M709214200","article-title":"Biochemical and structural insights into bacterial organelle form and biogenesis","volume":"283","author":"JB Parsons","year":"2008","journal-title":"J Biol Chem"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1002\/biot.201000181","article-title":"Prokaryotic gene clusters: a rich toolbox for synthetic biology","volume":"5","author":"M Fischbach","year":"2010","journal-title":"Biotechnol J"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"17729","DOI":"10.1074\/jbc.M112.355305","article-title":"Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly","volume":"287","author":"JN Kinney","year":"2012","journal-title":"J Biol Chem"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1002\/pro.2196","article-title":"Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria","volume":"22","author":"J Jorda","year":"2013","journal-title":"Protein Sci"},{"key":"ref39","article-title":"The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly","volume":"1","author":"F Abdul-Rahman","year":"2013","journal-title":"J Phylogenetics Evol Biol"},{"key":"ref40","first-page":"205","article-title":"A new generation of homology search tools based on probabilistic inference","volume":"23","author":"SR Eddy","year":"2009","journal-title":"Genome Inform"},{"key":"ref41","unstructured":"Sayers E (2010) Entrez Programming Utilities Help [Internet]. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK25501\/\" xlink:type=\"simple\">http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK25501\/<\/ext-link>. Accessed 9 February 2014."},{"key":"ref42","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s11120-006-9122-4","article-title":"Complete nucleotide sequence of the freshwater unicellular cyanobacterium <italic>Synechococcus elongatus<\/italic> PCC 6301 chromosome: gene content and organization","volume":"93","author":"C Sugita","year":"2007","journal-title":"Photosynth Res"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1128\/JB.186.3.623-630.2004","article-title":"A Novel Evolutionary Lineage of Carbonic Anhydrase (\u03b5 Class) Is a Component of the Carboxysome Shell","volume":"186","author":"AK-C So","year":"2004","journal-title":"J Bacteriol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1093\/jxb\/erg076","article-title":"CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution","volume":"54","author":"MR Badger","year":"2003","journal-title":"J Exp Bot"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1128\/JB.01151-06","article-title":"PduL is an evolutionarily distinct phosphotransacylase involved in B12-dependent 1,2-propanediol degradation by <italic>Salmonella enterica<\/italic> serovar typhimurium LT2","volume":"189","author":"Y Liu","year":"2007","journal-title":"J Bacteriol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1042\/BJ20090780","article-title":"Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in <italic>Clostridium kluyveri<\/italic>","volume":"423","author":"D Heldt","year":"2009","journal-title":"Biochem J"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"ME Smoot","year":"2011","journal-title":"Bioinformatics"},{"key":"ref49","article-title":"Graph clustering by flow simulation","author":"SM Van Dongen","year":"2001","journal-title":"Universiteit Utrecht"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1186\/1471-2105-12-436","article-title":"<italic>clusterMaker<\/italic>: a multi-algorithm clustering plugin for Cytoscape","volume":"12","author":"JH Morris","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/978-1-61779-361-5_15","article-title":"Using MCL to extract clusters from networks","volume":"804","author":"S Van Dongen","year":"2012","journal-title":"Methods Mol Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nature12352","article-title":"Insights into the phylogeny and coding potential of microbial dark matter","volume":"499","author":"C Rinke","year":"2013","journal-title":"Nature"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkr1044","article-title":"IMG: the Integrated Microbial Genomes database and comparative analysis system","volume":"40","author":"VM Markowitz","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"RC Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench","volume":"25","author":"AM Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"ref57","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":"S Guindon","year":"2010","journal-title":"Syst Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"W465","DOI":"10.1093\/nar\/gkn180","article-title":"Phylogeny.fr: robust phylogenetic analysis for the non-specialist","volume":"36","author":"A Dereeper","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-2148-10-8","article-title":"BLAST-EXPLORER helps you building datasets for phylogenetic analysis","volume":"10","author":"A Dereeper","year":"2010","journal-title":"BMC Evol Biol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated Profile HMM Searches","volume":"7","author":"SR Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"e243","DOI":"10.7717\/peerj.243","article-title":"PhyloSift: phylogenetic analysis of genomes and metagenomes","volume":"2","author":"AE Darling","year":"2014","journal-title":"PeerJ"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 \u2013 approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PLoS One"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1093\/nar\/gkh293","article-title":"ARB: a software environment for sequence data","volume":"32","author":"W Ludwig","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"W475","DOI":"10.1093\/nar\/gkr201","article-title":"Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy","volume":"39","author":"I Letunic","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1128\/JB.06444-11","article-title":"Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D","volume":"194","author":"EW Roberts","year":"2012","journal-title":"J Bacteriol"},{"key":"ref66","article-title":"Protein Content of Polyhedral Organelles Involved in Coenzyme B 12 -Dependent Degradation of 1, 2-Propanediol in Salmonella enterica Serovar Typhimurium Protein Content of Polyhedral Organelles Involved in Coenzyme B 12 -Dependent Degradation of 1, 2-Pr","volume":"187","author":"GD Havemann","year":"2003","journal-title":"J Bacteriol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"2217","DOI":"10.1016\/j.jmb.2014.02.025","article-title":"Assembly of robust bacterial microcompartment shells using building blocks from an organelle of unknown function","volume":"426","author":"JK Lassila","year":"2014","journal-title":"J Mol Biol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"7546","DOI":"10.1074\/jbc.M510464200","article-title":"The structure of \u03b2-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two","volume":"281","author":"MR Sawaya","year":"2006","journal-title":"J Biol Chem"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"7973","DOI":"10.1074\/jbc.M113.531236","article-title":"Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase\/oxygenase (RuBisCO) assembly factor in the \u03b1-carboxysome","volume":"289","author":"NM Wheatley","year":"2014","journal-title":"J Biol Chem"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"5778","DOI":"10.1128\/jb.175.18.5778-5784.1993","article-title":"Nucleotide sequence and functional analysis of CbbR, a positive regulator of the Calvin cycle operons of <italic>Rhodobacter sphaeroides<\/italic>","volume":"175","author":"JL Gibson","year":"1993","journal-title":"J Bacteriol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"5224","DOI":"10.1128\/jb.173.16.5224-5229.1991","article-title":"<italic>rbcR<\/italic>, a gene coding for a member of the LysR family of transcriptional regulators, is located upstream of the expressed set of ribulose 1,5-bisphosphate carboxylase\/oxygenase genes in the photosynthetic bacterium <italic>Chromatium vinosum<\/italic>","volume":"173","author":"AM Viale","year":"1991","journal-title":"J Bacteriol"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1128\/jb.175.4.1019-1025.1993","article-title":"Specific binding of <italic>Thiobacillus ferrooxidans<\/italic> RbcR to the intergenic sequence between the <italic>rbc<\/italic> operon and the <italic>rbcR<\/italic> gene","volume":"175","author":"T Kusano","year":"1993","journal-title":"J Bacteriol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1126\/science.1186090","article-title":"Spatially ordered dynamics of the bacterial carbon fixation machinery","volume":"327","author":"DF Savage","year":"2010","journal-title":"Science"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s11120-010-9608-y","article-title":"Inorganic carbon transporters of the cyanobacterial CO2 concentrating mechanism","volume":"109","author":"GD Price","year":"2011","journal-title":"Photosynth Res"},{"key":"ref75","article-title":"Bioinformatic Analysis of the Distribution of Inorganic Carbon Transporters and Prospective Targets for Bioengineering to Increase Ci uptake by Cyanobacteria","author":"SB Gaudana","journal-title":"Photosynth Res"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1073\/pnas.0910866107","article-title":"Structural basis of the oxidative activation of the carboxysomal \u03b3-carbonic anhydrase, CcmM","volume":"107","author":"KL Pe\u00f1a","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1104\/pp.110.154948","article-title":"Functional Cyanobacterial \u03b2-Carboxysomes Have an Absolute Requirement for Both Long and Short Forms of the CcmM Protein","volume":"153","author":"BM Long","year":"2010","journal-title":"Plant Physiol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1099\/00221287-136-5-887","article-title":"Cobalamin-dependent 1,2-propanediol utilization by <italic>Salmonella typhimurium<\/italic>","volume":"136","author":"RM Jeter","year":"1990","journal-title":"J Gen Microbiol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1099\/mic.0.27755-0","article-title":"Biochemical evidence that the <italic>pduS<\/italic> gene encodes a bifunctional cobalamin reductase","volume":"151","author":"EM Sampson","year":"2005","journal-title":"Microbiology"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"2805","DOI":"10.1093\/bioinformatics\/bti418","article-title":"MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems","volume":"21","author":"V Anantharaman","year":"2005","journal-title":"Bioinformatics"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"5010","DOI":"10.1073\/pnas.0734105100","article-title":"Molecular characterization of the 1,3-propanediol (1,3-PD) operon of <italic>Clostridium butyricum<\/italic>","volume":"100","author":"C Raynaud","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"6634","DOI":"10.1128\/jb.174.20.6634-6643.1992","article-title":"Autogenous regulation of ethanolamine utilization by a transcriptional activator of the <italic>eut<\/italic> operon in <italic>Salmonella typhimurium<\/italic>","volume":"174","author":"DM Roof","year":"1992","journal-title":"J Bacteriol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"4435","DOI":"10.1073\/pnas.0812194106","article-title":"Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in <italic>Enterococcus faecalis<\/italic>","volume":"106","author":"KA Fox","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"5937","DOI":"10.1128\/JB.00428-07","article-title":"<italic>Escherichia coli<\/italic> malic enzymes: two isoforms with substantial differences in kinetic properties, metabolic regulation, and structure","volume":"189","author":"FP Bologna","year":"2007","journal-title":"J Bacteriol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"e00248","DOI":"10.1128\/mBio.00248-11","article-title":"The <italic>Escherichia coli<\/italic> protein YfeX functions as a porphyrinogen oxidase, not a heme dechelatase","volume":"2","author":"HA Dailey","year":"2011","journal-title":"MBio"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"e48360","DOI":"10.1371\/journal.pone.0048360","article-title":"Structural insight into the <italic>Clostridium difficile<\/italic> ethanolamine utilisation microcompartment","volume":"7","author":"AC Pitts","year":"2012","journal-title":"PLoS One"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/S0928-8244(02)00448-0","article-title":"Comparison of the genome sequences of <italic>Listeria monocytogenes<\/italic> and <italic>Listeria innocua<\/italic>: clues for evolution and pathogenicity","volume":"35","author":"C Buchrieser","year":"2003","journal-title":"FEMS Immunol Med Microbiol"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1128\/JB.188.2.556-568.2006","article-title":"Identification of Listeria monocytogenes Genes Contributing to Intracellular Replication by Expression Profiling and Mutant Screening","volume":"188","author":"B Joseph","year":"2006","journal-title":"J Bacteriol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"7073","DOI":"10.1128\/AEM.01074-08","article-title":"Exogenous or L-rhamnose-derived 1,2-propanediol is metabolized via a <italic>pduD<\/italic>-dependent pathway in <italic>Listeria innocua<\/italic>","volume":"74","author":"J Xue","year":"2008","journal-title":"Appl Environ Microbiol"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1099\/mic.0.2006\/004747-0","article-title":"Identification of novel genes in genomic islands that contribute to <italic>Salmonella typhimurium<\/italic> replication in macrophages","volume":"153","author":"J Klumpp","year":"2007","journal-title":"Microbiology"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1006\/jmbi.2000.3824","article-title":"Structural and biochemical investigations of the catalytic mechanism of an NADP-dependent aldehyde dehydrogenase from <italic>Streptococcus mutans<\/italic>","volume":"300","author":"D Cobessi","year":"2000","journal-title":"J Mol Biol"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"2592","DOI":"10.1021\/bi00008a025","article-title":"Investigation of the Active Site Cysteine Residue of Rat Liver Mitochondrial Aldehyde Dehydrogenase by Site-Directed Mutagenesis","volume":"34","author":"J Farres","year":"1995","journal-title":"Biochemistry"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1128\/JB.01283-07","article-title":"A multiprotein bicarbonate dehydration complex essential to carboxysome function in cyanobacteria","volume":"190","author":"SS-W Cot","year":"2008","journal-title":"J Bacteriol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/nrm3392","article-title":"New lives for old: evolution of pseudoenzyme function illustrated by iRhoms","volume":"13","author":"C Adrain","year":"2012","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"5071","DOI":"10.1128\/JB.00575-10","article-title":"Characterization of the PduS cobalamin reductase of <italic>Salmonella enterica<\/italic> and its role in the Pdu microcompartment","volume":"192","author":"S Cheng","year":"2010","journal-title":"J Bacteriol"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"e14009","DOI":"10.1371\/journal.pone.0014009","article-title":"Characterisation of PduS, the <italic>pdu<\/italic> metabolosome corrin reductase, and evidence of substructural organisation within the bacterial microcompartment","volume":"5","author":"JB Parsons","year":"2010","journal-title":"PLoS One"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"37838","DOI":"10.1074\/jbc.M110.160580","article-title":"Structural insight into the mechanisms of transport across the <italic>Salmonella enterica<\/italic> Pdu microcompartment shell","volume":"285","author":"CS Crowley","year":"2010","journal-title":"J Biol Chem"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"21307","DOI":"10.1073\/pnas.1215689109","article-title":"Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme","volume":"109","author":"S Craciun","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1099\/00221287-95-1-173","article-title":"Microbial Metabolism of Amino Alcohols. Ethanolamine Catabolism Mediated by Coenzyme B12-dependent Ethanolamine Ammonia-Lyase in <italic>Escherichia coli<\/italic> and <italic>Klebsiella aerogenes<\/italic>","volume":"95","author":"FA Scarlett","year":"1976","journal-title":"J Gen Microbiol"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1080\/10409230701829169","article-title":"The Radical SAM Superfamily","volume":"43","author":"PA Frey","year":"2008","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1128\/JB.183.5.1577-1584.2001","article-title":"Functional genomic, biochemical, and genetic characterization of the <italic>Salmonella pduO<\/italic> gene, an ATP:cob(I)alamin adenosyltransferase gene","volume":"183","author":"V Johnson CL","year":"2001","journal-title":"J Bacteriol"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"4340","DOI":"10.1128\/JB.00137-06","article-title":"Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium \u201c<italic>Roseburia inulinivorans<\/italic>.\u201d","volume":"188","author":"KP Scott","year":"2006","journal-title":"J Bacteriol"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1007\/BF00423073","article-title":"Electron microscopic study on the quaternary structure of the isolated particulate alcohol-acetaldehyde dehydrogenase complex and on its identity with the polygonal bodies of <italic>Clostridium kluyveri<\/italic>","volume":"120","author":"R Lurz","year":"1979","journal-title":"Arch Microbiol"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"2128","DOI":"10.1073\/pnas.0711093105","article-title":"The genome of <italic>Clostridium kluyveri<\/italic>, a strict anaerobe with unique metabolic features","volume":"105","author":"H Seedorf","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1071\/BI9730547","article-title":"Ultrastructure of the Obligately Anaerobic Bacteria <italic>Clostridium kluyveri<\/italic> and <italic>Cl. acetobutylicum<\/italic>","volume":"26","author":"KY Cho","year":"1973","journal-title":"Aust J Biol Sci"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1007\/s00253-010-2924-5","article-title":"Genetic analysis around aminoalcohol dehydrogenase gene of <italic>Rhodococcus erythropolis<\/italic> MAK154: a putative GntR transcription factor in transcriptional regulation","volume":"89","author":"N Urano","year":"2011","journal-title":"Appl Microbiol Biotechnol"},{"key":"ref107","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1111\/j.1472-765X.2006.01970.x","article-title":"A novel NADP+-dependent L-1-amino-2-propanol dehydrogenase from <italic>Rhodococcus erythropolis<\/italic> MAK154: a promising enzyme for the production of double chiral aminoalcohols","volume":"43","author":"M Kataoka","year":"2006","journal-title":"Lett Appl Microbiol"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1007\/s002030050635","article-title":"Methylglyoxal production in bacteria: suicide or survival?","volume":"170","author":"GP Ferguson","year":"1998","journal-title":"Arch Microbiol"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/S0021-9258(18)55739-2","article-title":"Enzymatic synthesis and breakdown of desoxyribose phosphate","volume":"196","author":"E Racker","year":"1952","journal-title":"J Biol Chem"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/0304-4165(70)90048-6","article-title":"Regulation of ribose metabolism in <italic>Escherichia coli<\/italic>: II. Evidence for two ribose-5-phosphate isomerase activities","volume":"208","author":"J David","year":"1970","journal-title":"Biochim Biophys Acta - Gen Subj"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1128\/jb.178.4.1003-1011.1996","article-title":"Ribose catabolism of <italic>Escherichia coli<\/italic>: characterization of the <italic>rpiB<\/italic> gene encoding ribose phosphate isomerase B and of the <italic>rpiR<\/italic> gene, which is involved in regulation of <italic>rpiB<\/italic> expression","volume":"178","author":"KI S\u00f8rensen","year":"1996","journal-title":"J Bacteriol"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.jbiotec.2008.09.012","article-title":"Novel substrates of a ribose-5-phosphate isomerase from <italic>Clostridium thermocellum<\/italic>","volume":"139","author":"R-Y Yoon","year":"2009","journal-title":"J Biotechnol"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"e87353","DOI":"10.1371\/journal.pone.0087353","article-title":"The candidate phylum <italic>Poribacteria<\/italic> by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features","volume":"9","author":"J Kamke","year":"2014","journal-title":"PLoS One"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/nar\/gki232","article-title":"A novel method for accurate operon predictions in all sequenced prokaryotes","volume":"33","author":"MN Price","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref115","unstructured":"Chuang L-Y, Chiang Y-C, Yang C-H (2012) A Quantum Genetic Algorithm for Operon Prediction. 2012 IEEE 26th International Conference on Advanced Information Networking and Applications. IEEE. pp. 269\u2013275. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/ieeexplore.ieee.org\/lpdocs\/epic03\/wrapper.htm?arnumber=6184880\" xlink:type=\"simple\">http:\/\/ieeexplore.ieee.org\/lpdocs\/epic03\/wrapper.htm?arnumber=6184880<\/ext-link>. Accessed 23 May 2014."},{"key":"ref116","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1093\/nar\/30.10.2212","article-title":"Connected gene neighborhoods in prokaryotic genomes","volume":"30","author":"IB Rogozin","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1093\/bioinformatics\/btp027","article-title":"Detecting gene clusters under evolutionary constraint in a large number of genomes","volume":"25","author":"X Ling","year":"2009","journal-title":"Bioinformatics"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/j.molcel.2010.04.008","article-title":"Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement","volume":"38","author":"JB Parsons","year":"2010","journal-title":"Mol Cell"},{"key":"ref119","doi-asserted-by":"crossref","first-page":"7157","DOI":"10.1128\/JB.00838-09","article-title":"Comparative genomics of ethanolamine utilization","volume":"191","author":"O Tsoy","year":"2009","journal-title":"J Bacteriol"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.cbpa.2009.11.029","article-title":"Recent progress in stereoselective synthesis with aldolases","volume":"14","author":"P Clap\u00e9s","year":"2010","journal-title":"Curr Opin Chem Biol"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"15971","DOI":"10.1073\/pnas.0503868102","article-title":"Combining two genomes in one cell: stable cloning of the <italic>Synechocystis<\/italic> PCC6803 genome in the <italic>Bacillus subtilis<\/italic> 168 genome","volume":"102","author":"M Itaya","year":"2005","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003898","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T15:08:21Z","timestamp":1650467301000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003898"}},"subtitle":[],"editor":[{"given":"Mark M.","family":"Tanaka","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,10,23]]},"references-count":121,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2014,10,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003898","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,10,23]]}}}