Sequences: (via blast, fasta, text search)
- GenBank (NR, GBALL, GBMAM, GBBCT, GBENV, GBEST, GBGSS, GBHTC, GBHTG, GBPAT, GBINV, GBPHG, GBPLN, GBPRI, GBROD, GBSTS, GBSYN, GBUNA, GBVRL, GBVRT)
- Uniprot (SwissProt, TREMBL)
- REFSEQ NCBI's curated collection of DNA, RNA, and Protein Sequences
- Third Party Annotation NCBI's database of inference- and experiment- based annotations
- UniParc UniProt's archive of all reported protein sequences
- UniMES UniProt's database of Metagenomic and Environmental Samples
- Blocks (via Blimps) The Blocks Database is no longer updated by FHCRC.
- Pfam (via HMMPFAM and RPSBLAST)
- Prints (via FingerPRINTScan)
- Prosite ( via PFSCAN; PFSEARCH; PPSEARCH; PROSEARCH)
- CDD (via RPSBLAST). A superset including NCBI-curated domains and data imported from Pfam, SMART, COG, and PRK
- COG (via RPSBLAST). COG database of orthologous protein families focusing on prokaryotes. See Cognitor for an alternative.
- KOG (via RPSBLAST). The eukaryotic counterpart to COGs. KOGs are not included in the CDD superset.
- PRK (via RPSBLAST). Reference Sequence proteins encoded by complete prokaryotic and chloroplast plasmids and genomes.
- SMART (via RPSBLAST) Very Short SMART Peptides and SMART Superfamilies are not included in this DB.
- PDBFINDER2 (via text search). Searchable database of PDB metadata and structure features.
- PDB (via text search and the Sirius browser). Universal database of protein structure models.