About MMTB

The Metano Modeling Toolbox (MMTB) was developed for an enhanced user experience when building n models. If you want to know more about n, the reaction format, and all of the features please visit the metano website.

The regular search

There are three kinds of requests on the general search page:

1. Reactions

There are different ways to get information about reactions from MMTB. The first one is to enter parts of a reaction in standard reaction format:

optional_reaction_name : [1] educt1 + [1] educt2 <=> [1] product1 + [1] product2

Each part of this query is optional, but it must contain at least one metabolite and an operator (+ or =) or an arrow to be recognized as reaction query.

You can also search for reactions by entering the EC number of a catalyzing enzyme (see the website of the IUBMBfor more information) or by searching for BRENDA, KEGG or MetaCyc-IDs.

Example:

The reaction of the malate dehydrogenase

(S)-malate + NAD+ = oxaloacetate + NADH

can be found by either typing

  • parts of the reaction ( malate = oxaloacetate or L-malate =),
  • the EC-number ( 1.1.1.37), or
  • the database ID (e.g. the MetaCyc-ID MALATE-DEH-RXN).

Depending on which request method is used, you will get additional informations, such as other related reactions for the requested metabolites, other EC numbers for this reaction or other databases that share the informations.

Note that the direction of all reactions is NOT correctly assigned since it depends on various external factors, such as temperature and pH. For this reason, each reaction is displayed as reversible reaction.
Downloads and copy to clipboard:

The result can be downloaded as reaction file in metano format. The reaction names consist of the pathway - if the enzyme is associated to a pathway - all known EC-numbers for this reaction, and one of the known database IDs as identifiers.

Additionally, it is possible to copy a single reaction in the same format as described above to the clipboard by clicking on the icon on the left-hand side of the reaction.

Relevance Score

When a certain organism is selected from the dropdown list, the EnzymeDetector relevance score is shown for each enzyme. This score is a indication of the reliabilty of this annotation.

Display style:

The result table is sorted by the relevance score and the number of external database entries, respectively. If the relevence score is higher than a 30% gene threshold, the score is displayed in bold. This threshold is calculated for each organism individually by the EnzymeDetector and underlies the assumption, that 30% of all genes of an organism have an enzymatic function (Quester and Schomburg, 2011). If none of the enyzmes coding for the reactions is annotated for the organism of interest, the entries are highlighted in red.

2. Metabolites

If a single metabolite is searched, MMTB gives you information about the recommended name and all available synonyms. If the information is available, it will also show the molecular weight and chemical structure and links to the BRENDA ligand page for further information.

3. Regular Expressions

If a metabolite query contains either one of the following regex characters ( *, $, ^) or begins and ends with /, the query is handled as regular expression search. The result table gives information about all metabolite synonyms that matched the regular expression, and their respective recommended name.

For example, the query *malategives an overview of all metabolites that end with malateand *malate*returns all metabolites that contain malateon any position.

The search API

The MMTB provides a basic API that allows to link directly to any of the above mentioned search pages:

http://mmtb.tu-bs.de/search/

The could be replaced by your reaction, metabolite or RegEx query of interest.

The pathway search

The Pathway search provides an additional query method.

In the pathway section of the MMTB, a BRENDA pathway can be choosen from a dropdown list. The result shows all reactions that are associated to this pathway. The result table gives the same information like normal reaction queries and can also be downloaded as reaction file.

The Analysis

The last important part of the MMTB is the analyis page. It allows to perform some basic n methods online. At the moment, the MMTB features Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), and a metabolite replacement tool (BETA!). Metabolite Flux Minimization (MFM) will be included soon!

To perform an analysis, upload your metano model and a scenario file, choose a analysis method and click on "Upload & Analyze". The resulting flux distribution file can be saved on your computer once the analysis is complete.

Additionally, the MMTB is able to create a scatter plot to compare two flux distributions, obtained by either FBA/MOMA, FVA, or MFM. he flux distributions can be either CSV or TXT format. The scatter plot can be adjusted for your personal needs regarding display style, point and axis labeling, significances, and error bars. You can download the scatter plot by right-clicking on it and choosing "save as...".