The Map Organism tool lets you submit your own proteome or amino acid sequences and compare them against a reference functional repertoire from 8,906 microbial organisms. The result is a functional profile of your query, including GO term and EC number annotations, alongside a ranked list of the most similar organisms in the database.
Go to the Map Organism page. You can provide your sequences in two ways:
Paste sequences — copy the contents of your multi-FASTA file directly into the text box on the page.
Upload a file — use the file upload option to select a FASTA proteome file from your computer.
You can also enter an optional email address to receive a notification with a direct link to your results once the job finishes. This is recommended for larger proteomes, as processing may take several minutes.
Click Submit. You will be redirected to a status page showing the progress of your job. Bookmark this page if you did not provide an email, as it is your way back to the results.
Once your job finishes you are taken to the results page. At the top is a brief summary showing how many of your proteins were mapped to known functions. Below that are two tables.
This table lists every function that one or more of your query proteins was mapped to. Each row includes:
ID — the Fusion function identifier.
Functional Annotation — a description of the function, including GO terms (e.g. GO:0003674) and EC numbers (e.g. EC 1.1.1.1) where available.
HFSP — the homology-derived functional similarity of proteins, a confidence score for the function assignment.
Mapped Query Proteins — the number of your input proteins assigned to this function; click the info button in this column to open a pop-up listing the specific protein identifiers from your FASTA input.
The table is searchable using the box above it. Enter space-separated terms to filter rows using AND logic. You can search across function IDs, text annotations, GO IDs, GO term names, EC numbers, and mapped protein IDs. Search for broader EC classes by substituting hyphen ("-") characters for more specific digits (e.g., "1.1.-.-"). GO term search does not include ancestor terms.
This table ranks reference organisms by their functional similarity to your query. It includes habitat, temperature, and oxygen preference metadata for several organisms. Select organisms in the table, and then display the functions they share with your query by pressing Display Core Functional Repertoire.
The Mapped Functions table can be exported in full as a CSV file containing all functional annotations for your proteome.
1. Click CSV above the Mapped Functions table to save the table as a comma-separated value (.csv) file.
2. Open the file in a spreadsheet application or parse it programmatically. The file includes the molecular function GO terms and EC numbers you can use for downstream enrichment analyses or pathway mapping as well as the the sources for the GO terms or EC numbers. The Fusion-SP source label indicates the terms were pulled from Swiss-Prot (SP) at all evidence levels following alignment of the Fusion reference proteins to SP, taking the match with highest HFSP≥14 per Fusion reference protein. The LLM label indicates the terms were extracted with an LLM (Opus 5) from the text annotation. LLM-extracted GO terms were translated to EC numbers.
Fusion-SP EC numbers and GO terms downloaded from Mapped Functions table rows (for individual Fusion functions) include the number and fraction of unique SP matches with the corresponding annotation for the Fusion function.