The major goal of the "Explore Pathways" section is to check the conservation rate of general metabolic pathways represented by a chain of known enzymatic reactions (with full EC numbers only) among your particular selection of genomes (see details on Species selection below).

Available pathways from KEGG or MetaCyc should be chosen in drop-down menus (form 1), identified using keywords (form 2) or a set of included EC numbers (form 3).

• See examples: colorized pathway; summery table; full EC table
• Select your genomes here or click on "Species selection" in the top menu.
• Go to the forms here to load a pathway or click on "Explore pathways" in the top menu.

For each EC number, you can access to the content of a set of ortholog groups harboring at least one protein from any of your Species of interest and to the sequences of the corresponding proteins (fasta formatted).

Results rely on the EC numbers attributed to each orthology group of FUNGIpath. Standard pathways from KEGG or MetaCyc should be analysed for their representation in fungi along with BioPax2 formatted pathways (Please, follow the help section to write your own pathway and load it in form 4).

According to the wide choice of combination of Species, new searches should take a while. Already done searches are permanantly stored on our server.

The "Search for orthologs" section is dedicaced to the exploration of FUNGIpath orthology groups.

Groups matching with keywords (annotated groups only): Keywords will be searched in group function or EC numbers definition (form 1).

• See examples: filtered group table
• Go to form 1 or click on "Search for orthologs" in the top menu.

Search orthologs of your protein (FUNGIpath species only): You will get a table presenting orthologs of the submitted protein (form 2). Prefer the sequence submission (form 3) if you dont know the protein ID.

See examples: Orthology group table
• Go to form 2 or click on "Search for orthologs" in the top menu.

Search for the closiest orthology group of your protein: The amino-acids sequence of the submitted protein (any origin) will be compared to HMM profiles of orthology groups and the best hit reported.

See examples: Orthology group table
• Go to form 3 or click on "Search for orthologs" in the top menu.

Whole genome approach: Orthologs tables show groups harboring proteins of your selection of genomes along with their inferred function and EC numbers (form 4). Tables should be very big but are downloadable and should be filtered using various criteria.

• See an example: Whole genome table
• Select your species here or click on "Species selection" in the top menu
• Go to form 1 or click on "Search for orthologs" in the top menu.

According to the wide choice of combination of Species, new searches should take a while. Already done calculs are permanantly stored on our server.

By default all FUNGIpath species are selected.

Select your own species here:

• Click on "Change the status of all genomes to allowed".
• Change the status of your species of interest to "selected".

When all other species are allowed, queries will return orthology groups containing any proteins from your selected species. If you are interested in more specific genes, you can change the status of some "allowed" species to "excluded" to restrict results to orthology groups without orthologs in excluded species.