Draft reconstruction generation

Firstly, you need to have a close related model organism whose metabolic reconstruction has been built already.

Then you need to prepare a blank reconstruction containing gene information of your interest strain. This file can be generated by GBKParser (http://sb.nhri.org.tw/GEMSiRV/en/GBKParser). However, you need to add the corresponding orthologous genes to the column of Ref-BLAST.

For example, we want to draft a reconstruction of Salmonella enteric subsp. Enteric serovar Typhimurium str. LT2 (SLT2) by mapping to the reconstruction model iAF1260 of Escherichia coli str. K-12 substr. MG1655 (ECO).

Therefore, we download the gbk files of these two strains from RefSeq (http://www.ncbi.nlm.nih.gov/RefSeq). With available NC_003197.gbk and NC_000913.gbk files for SLT2 and ECO respectively, we then use GBKParser to parse basic gene information and amino acid sequences. In addition, we download the metabolic model iAF1260 from BiGG (http://bigg.ucsd.edu/) and modify it with TextReplacer (http://sb.nhri.org.tw/GEMSiRV/en/TextReplacer). The ready-to-use model can be found and downloaded from http://sb.nhri.org.tw/GEMSiRV/en/Metabolic_Models.

The amino acid sequence files for SLT2 and ECO can be used to generate the reciprocal orthologous-gene pairs by BLASTP or other available software. For example, MrBac (http://sb.nhri.org.tw/MrBac) can be used to generate the needed file. However, the detailed procedure is not described here.

The basic gene information parsed from the gbk file is outputted to a spreadsheet file, e.g. NC_003197.gbk.xls, which can be imported into GEMSiRV directly. Right click on Model Databases to Import spreadsheet (.xls).

Original spreadsheet file:

Required fields

Gene Index table of the imported blank reconstruction (NC_003197.gbk-blast.xls):

Empty Reaction Index table of the imported blank reconstruction:

Right click on the blank reconstruction to Draft a reconstruction by choosing SBML_export_E.coli iAF1260_out.xml as the reference model.

The reactions in the reference reconstruction are classified into two indices (Reaction Index and _Invalid Reaction Index) for the draft reconstruction: one list containing reactions whose associated orthologous genes are present in the blank reconstruction and conform to Boolean statements as described in the reference reconstruction, the other containing those reactions with unknown gene-reaction associations or reactions whose orthologous genes are absent and let to disagree Boolean statements.