This document describes in detail the results of the ReTrace analysis of T. reesei amino acid biosynthesis pathways as described in the manuscript
P. Jouhten, E. Pitkänen, T. Pakula, M. Saloheimo, M. Penttilä and H. Maaheimo: 13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. Submitted, 2009.Result files can be accessed by the link below.
ReTrace generates result files of three different types: a query summary, query HTML result, query text result and pathway result files. In the following the contents of these files are explained.
Most tables in results are sortable by clicking column headings.
In addition to pathways discussed in the manuscript, the results include also pathways for other metabolites. For example, alanine biosynthesis pathways starting from both glucose and pyruvate are provided.
The query summary file contains a table which summarizes ReTrace results for each pathway query performed. The table includes queries from amino acid precursors to amino acids, as described in the manuscript. Additionally, other queries are reported. For instance, amino acids queries where glucose was assigned the source metabolite were performed and are reported here.
Each line in the summary table corresponds to a single pathway query. The two hyperlinks for each entry link to query HTML and text result files, which are described in detail below.
The table gives the following information about query results.
Query HTML result files, accessible from the query summary table, give information about each result pathway found for the query, and provide links to a more detailed description of each pathway (pathway result file).
Query HTML result file contains a table with the following columns.
Query text result files provide the same information as query HTML result files. Additionally, for each pathway, the individual KEGG RPAIR and reaction entries are given. Moreover, lines prefixed with "#" report the query parameters given to ReTrace, in addition to the total query time.
Each pathway result file reports an individual metabolic pathway in html format.
Each file begins with a graphical description of the composite mapping corresponding to the pathway by giving molecular structures for source and target metabolites. In each image of a molecule, green circles denote atoms that are involved in the composite mapping. Further, the composite mapping is specified under the images as a text string. Note: images are drawn with an external program located on the server sysdb.cs.helsinki.fi.
KEGG RPAIR entries used on the pathway are listed in a table, one entry per line. For each entry, the table contains the following data.
Finally, the file concludes with a pathway diagram. Reactions are drawn as boxes, metabolites as ellipses. Reactions have been color-coded as in the table. Source and target metabolites have been color-coded green and yellow, respectively.