Table 4.
Databases used by the PAM tools
| Name | Description | Reference |
|---|---|---|
| UNIPROT | Protein sequences and functions | (67) |
| KEGG | Molecular interaction networks | (37) |
| CDD | Conserved domain database | (33) |
| PDB | 3D structures database | (68) |
| SCOP | Protein 3D domain database | (69) |
| PROSITE | Functional motifs and profiles derived from SWISSPROT | (70) |
| PRINTS | Manually derived functional motifs | (36) |
| SMART | Motifs of genetically mobile domains | (8) |
| PFAM | Protein family domains | (71) |
| TIGRFAMs | Similar to PFAM | (72) |
| SUPERFAMILY | Families of proteins of known 3D structures | (62) |
| GENE3D | Protein families and domain architectures in complete genomes | (63) |
| PANTHER | Protein families subdivided into functionally related subfamilies | (61) |
| PRODOM | Automatically generated protein domain families | (64) |