Table 1 Attributes of a minimotif definition
# | Attribute1 | Valid values and description |
|---|---|---|
1 | Motif sequence type | (Consensus, instance, PSSM) type of sequence definition |
2 | Motif sequence | Any consensus, instance, or PSSM describing a minimotif protein sequence |
3 | Required modification | description of chemical change to minimotif sequence |
4 | Motif source name | The name of protein or peptide that contains the minimotif |
5 | Motif source accession number | Swiss-Prot, RefSeq accession numbers for protein sequences containing the minimotif |
6 | Motif start position | Integer start position of the minimotif in motif source accession number |
7 | Motif source type | (Peptide and/or protein) indicates whether minimotif was investigated as a peptide fragment or in a protein domain |
8 | Activity | (binds, modifies, requires, traffics) the action of the minimotif |
9 | Subactivity | A more detailed description |
10 | Activity modification | Description of activity that covalently changes a minimotif sequence |
11 | Target name | The name of the molecule that acts upon the minimotif |
12 | Target accession number | If the target is a protein, the Swiss-Prot or RefSeq accession number(s) for Target protein sequence(s). The target can be a complex |
13 | Target type | (Peptide and/or protein) indicates whether Target was investigated as a peptide fragment or in a protein domain |
14 | Target domain | (any domain in the CDD) protein domain in the minimotif Target |
15 | Target domain position | Integer that indicates the relative location of a domain relative to its N-terminus for proteins that have more than one copy of the same domain |
16 | Target site | Integer for site where a minimotif binds a molecule, if more than one site is known |
17 | Subcellular localization | Region of the cell where the minimotif activity occurs |
18 | Affinity | (Kd, IC50, Km) measurement of affinity of minimotif for its target |
19 | Structure | (PDB accession number) for a structure of the minimotif in complex with its target. A related attribute is 'related structures' of the minimotif source or target. |
20 | Experimental evidence | (X-ray, NMR, Phage display, peptide mapping, alanine scanning mutagenesis, evolutionary conservation, mutagenesis, modeling, deletion mapping, peptide binding, peptide competition, full-length protein, Surface Plasmon Resonance, ITC, SPOT array, Far-western, Co-immunoprecipitation, yeast 2-hyrbid, pulldown) different types of experimental evidence that supports a minimotif sentence. |
21 | Minimotif reference | (PubMed identifier or PDB accession number) indicates the references source(s) of the data supporting the minimotif definition |
22 | Database reference | Cross reference ID to other database that contains similar minimotif definition. |