protein-sequence-similarity-search

You can find homologous proteins by providing a raw amino-acid sequence or FASTA file as input. The tool searches sequence similarity databases using MMseqs2 to identify matching protein homologues and infer protein function.

MMseqs2 provides fast homologue searching via the ColabFold API, while BLAST offers a slower, comprehensive fallback through EBI. BLAST is used when MMseqs2 hits rate limits or when specific UniProt or structure databases are explicitly requested.

When MMseqs2 is rate-limited, the tool automatically falls back to EBI BLAST for your homology search. You can also explicitly request BLAST to query specific allowed UniProt or structure databases for comprehensive results.

Yes, you can use a FASTA file as input for a protein sequence similarity search. The tool interprets alignment metrics like E-value and sequence identity, producing ranked Markdown summaries and optional JSON files for follow-on analysis.

Yes, the EBI BLAST fallback supports strict allowed database codes. You can explicitly request BLAST to search specific UniProt or structure databases when you need more comprehensive coverage than the default MMseqs2 search provides.

A protein sequence search may fail if MMseqs2 is rate-limited and cannot connect, or if the input sequence format is invalid. The tool avoids hallucinated results and raw output parsing, ensuring only verified alignment metrics are reported.