RAVEN 2.0: a versatile platform for metabolic network reconstruction and a case study on Streptomyces coelicolor

Supplementary Information to the paper "RAVEN 2.0: a versatile platform for metabolic network reconstruction and a case study on <i>Streptomyces coelicolor</i>", as posted on bioRxiv.<br>RAVEN 2.0 is available from GitHub.<br>Sco4 is available from GitHub.<br><b>S1 Data. Model structure after merging three <i>de novo</i> draft reconstructions.</b><b><br></b> <b>S1 Table. Mapping of reactions to <i>de novo </i>reconstructions.</b> To facilitate comparison of the existing iMK1208 model and the <i>de novo </i>reconstructions, iMK1208 reactions are mapped to their respective KEGG and MetaCyc counterparts.<br> <b>S2 Table. Association of metabolites to KEGG and MetaCyc identifiers. </b>To facilitate comparison of the existing iMK1208 model and the <i>de novo </i>reconstructions, iMK1208 metabolites are matched to their respective KEGG and MetaCyc identifiers.<br> <b>S3 Table. Reactions from the <i>de novo </i>draft models used in <i>Sco4</i> generation. </b>A set of reactions was selected from the <i>de novo</i> draft model for manual curation of the existing model towards <i>Sco4</i>.<br> <b>S4 Table. Missing gene-associations in that were filled by <i>de novo</i> reconstruction. </b>These reactions had no gene associated in iMK1208, but <i>de novo</i> reconstruction with RAVEN 2.0 identified the responsible genes.<br> <b>S5 Table. Spontaneous reactions included in <i>Sco4</i> model, as identified from MetaCyc.</b><b><br></b> <b>S6 Table. Transport reactions added to <i>Sco4</i> model based on MetaCyc-based reconstruction and manual curation.</b><b><br></b> <b>S7 Table: Complete list of invalid KEGG identifiers and their replacements.</b><b><br></b> <b>S8 Table. Comparison of growth media validation results between iMK1208 and Sco4. </b>The growth media validation on iMK1208 and Sco4 models. The culture and simulating conditions were described previously [28]. Predictions on iMK1208 and Sco4 showed identical results.<br> <b>S9 Table: Identification of putative essential genes from mutagenesis study and predictions from the iMK1208 and <i>Sco4</i> models. </b>Logical indicating whether a gene has been identified in any of the three analyses.<br> <b>S10 Table. Combined FSEOF results on the secondary metabolites included in <i>Sco4</i> model. </b>Target reactions identified for each of the secondary metabolites are indicated, together their gene association. Direction indicates whether a reaction is reversible and running in the forward direction (1), running in the reverse direction (-1), or is irreversible (0).<br> <b>S11 Table. Definition of RAVEN model structure fields. </b>Where applicable, corresponding COBRA model structure fields are indicated.<br> <b>S12 Table. Reaction identifier correspondence between KEGG and MetaCyc. </b>The mapping information was provided by MetaCyc and expanded using function linkMetaCycKEGGRxns. <b></b><br> <b>S13 Table. Metabolite identifier correspondence between KEGG and MetaCyc. </b>The mapping information was provided by MetaCyc.