FUNGIpath (iGenolevure version) is a web service dedicated to the exploration of yeasts (Saccharomycetales) metabolism.

FUNGIpath predicts groups of orthologous proteins in fungal genomes with the MaRiO pipeline (Reference here). Orthology groups are annotated with the FUNGIpath annotation pipeline based on Swiss-Prot and MetaCyc data. Fonctional annotations of groups allows an easy comparison of the metabolism whithin species represented in the associated database.

The 34 species for which data are currently available in the yeast version of FUNGIpath (v.1.0 - june 2015) are listed below:

Click on the box to see all FUNGIpath Species: Species table
SaccharomycetalesDipodascaceaeYarrowiaYarrowia lipolytica
SaccharomycetaceaeArxulaArxula adeninivorans
CandidaCandida albicans
Candida parapsilosis
CyberlindneraCyberlindnera fabianii
DebaryomycesDebaryomyces hansenii
EremotheciumAshbya gossypii
KazachstaniaKazachstania naganishii
KluyveromycesKluyveromyces lactis
KuraishiaKuraishia capsulata
LachanceaLachancea cidri
Lachancea dasiensis
Lachancea fantastica
Lachancea fermentati
Lachancea kluyveri
Lachancea lanzarotensis
Lachancea meyersii
Lachancea mirantina
Lachancea nothofagi
Lachancea quebecensis
Lachancea thermotolerans
Lachancea waltii
MillerozymaPichia sorbitophila
NakaseomycesCandida bracarensis
Candida castellii
Candida glabrata
Candida nivariensis
Nakaseomyces bacillisporus
Nakaseomyces delphensis
NaumovozymaNaumovozyma castellii
SaccharomycesSaccharomyces cerevisiae
TetrapisisporaTetrapisispora blattae
ZygosaccharomycesZygosaccharomyces bailii
Zygosaccharomyces rouxii

Explore pathways

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).

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.

Search for orthologs

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).

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.

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.

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.

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

Species selection

By default all FUNGIpath species are selected.

Select your own species here:

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.

 Retrieve orthology groups from our database IDs 

Some results of user's requests (explore pathways and "All groups of orthologous proteins corresponding to a taxonomic profile" are permanently stored on our server and should be reloaded via the corresponding forms. Group data are accessible with FUNGIpath IDS and the forms below:

  • Enter the FUNGIpath ID of a group of orthologs 

    Paste a group ID
    (i.e. 15)

  • Enter the FUNGIpath ID of a protein to display the orthologs group to which it belongs 

    Paste a gene ID
    (i.e. Afu5g06390)

  • Search FUNGIpath groups annotated with an EC number 

    Paste an EC number

Fungipath group annotations All sequences of an orthology group are annotated (when valuable data exist) with enzymatic activities (i.e. Enzyme Commission numbers), Gene Ontology Consortium IDs and explicite Protein fonction (as "Alpha-keto-glutarate dependent dioxygenase abh1"). Annotations, if any, are inferred by comparison of the whole group sequences with already characterised proteins from any sequenced genome.

References The MaRiO pipeline is described in the article: Pereira C, Denise A, Lespinet O (2014). A meta-approach for improving the prediction and the functional annotation of ortholog groups. BMC Genomics 2014;15:S16.

You can find the annotation pipeline and additional informations in the publication: FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. Grossetete S, Labedan B, Lespinet O. BMC Genomics 2010;11:81.