Target databases ================ The HMMER web service supports querying against a range of regularly updated sequence and HMM target databases. ------------------ Sequence databases ------------------ * Large, comprehensive sequence collection - `UniProt `_ - Comprehensive resource for protein sequence and annotation data produced by the Universal Protein Resource consortium. * Annotated sequences and determined 3D structures - `SwissProt `_ - Manually reviewed, high quality protein sequence and functional annotation - produced by UniProt. - `PDB `_ - Sequences with an experimentally determined structure. * Representative Sets - `Representative Proteomes `_ - Representative Proteomes (RPs) are determined by selecting one proteome from a representative proteome group containing similar proteomes calculated based on sequence co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold are available as target databases. More information on `Representative Proteomes `_ is available. The data set also includes model organisms and viral reference proteomes as defined by UniProt. The complete proteomes database comes from PIR. - `Reference Proteomes `_ - A set of proteomes from UniProt that gives broad coverage of the tree of life, and constitutes a representative cross-section of the taxonomic diversity to be found within UniProtKB. Produced by UniProt, in collaboration with Ensembl and the NCBI Reference Sequence collection. The default database is UniProt reference proteomes. --------------------- Profile HMM databases --------------------- * `Pfam `_ - A large comprehensive collection of protein families. ----------------- Search provenance ----------------- Clicking 'Search Details' at the top of the result table reveals a box that provides details of the search, including the query sequence (if applicable) and information regarding the date/release of the target databases, which should be recorded for future reference when trying to recreate the results, discussing with colleagues or reporting bugs.