P2CS-Web
Two-component systems, rebuilt for exploration
Documentation / Help
Quick guidance for browsing and protein-search workflows.
This page summarizes the current navigation logic and the main search-engine choices available in the protein search interface.
Protein Search Engines
All searches run against the local HK and RR cluster databases.
MMseq2 is the best default choice for interactive exploration and large local datasets.
blastp is available when you want the classical BLAST workflow. In the current interface, blastp defaults to blastp-fast with 4 threads to keep searches responsive on large databases.
DIAMOND is also available as an alternative protein-protein search engine.
blastp Task Modes
Use these modes depending on query length and expected similarity.
blastp: the standard protein-protein BLAST mode. It is usually the most conservative choice when you want sensitivity over speed.
blastp-fast: a faster variant that uses a larger seed word size. It is a good interactive default when you expect reasonably similar proteins and want shorter response times.
blastp-short: optimized for very short peptide queries, typically shorter than 30 amino acids. It is not the right default for full-length HK or RR proteins.