PMC:4301621 / 30161-31805 JSONTXT

{"project":"2_test","denotations":[{"id":"25582171-23624532-14905503","span":{"begin":147,"end":149},"obj":"23624532"},{"id":"25582171-22472172-14905504","span":{"begin":169,"end":171},"obj":"22472172"},{"id":"25582171-23236514-14905505","span":{"begin":198,"end":200},"obj":"23236514"},{"id":"25582171-14681372-14905506","span":{"begin":487,"end":489},"obj":"14681372"},{"id":"25582171-22472172-14905507","span":{"begin":676,"end":678},"obj":"22472172"},{"id":"25582171-23236514-14905508","span":{"begin":696,"end":698},"obj":"23236514"},{"id":"25582171-14568541-14905509","span":{"begin":926,"end":928},"obj":"14568541"},{"id":"25582171-17526522-14905510","span":{"begin":1067,"end":1069},"obj":"17526522"},{"id":"25582171-10592173-14905511","span":{"begin":1155,"end":1157},"obj":"10592173"},{"id":"25582171-17965431-14905512","span":{"begin":1202,"end":1204},"obj":"17965431"},{"id":"25582171-15534700-14905513","span":{"begin":1219,"end":1221},"obj":"15534700"},{"id":"25582171-15096640-14905514","span":{"begin":1398,"end":1400},"obj":"15096640"},{"id":"25582171-17517783-14905515","span":{"begin":1419,"end":1421},"obj":"17517783"},{"id":"25582171-16873501-14905516","span":{"begin":1432,"end":1434},"obj":"16873501"},{"id":"25582171-16381841-14905517","span":{"begin":1640,"end":1642},"obj":"16381841"}],"text":"The draft model was constructed by amassing reactions from the genome-scale metabolic models of genetically related organisms Aspergillus terreus [44], Pichia pastoris [45] and Yarrowia lipolytica [20]. Reactions were chosen based on orthologs shared between M. alpina and the three reference organisms identified by protein sequence similarity searches using BLAST. Protein sequences from A. terreus NIH 2624, P. pastoris GS 115 and Y. lipolytica CLIB 122 were downloaded from UniProt [46]. Open reading frame (ORF) information for M. alpina ATCC 32222 was provided by Yong Q. Chen based on sequencing results. The iJL1454 GSMM was used as a reference. Additionally, iLC915 [45] and iYL619_PCP [20] were also used for comparison since both models were concerned with lipid metabolism and overproduction. To ensure accuracy, only sufficiently similar orthologs with e-values ≤10−30 and sequence identities ≥40% were included [47]. To expand and update the draft model, the genome of M. alpina was re-annotated by submitting ORFs to the KAAS online annotation server [48]. Metabolic reactions absent from the draft model were added from the KEGG database [49] based on KAAS annotation results. MetaCyc [50] and BioPath [51] databases were used to judge reaction reversibility. Compartmentalization information assigned to reactions was determined by subcellular localization prediction tools CELLO [52] and WoLF PSORT. [53] BaCelLo [54] was also used for proteins that were difficult to determine with the other tools. Transport information was obtained by cross-referencing BLATSp searches and the Transporter Classification Database TCDB [55]."}