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Table 1 Attributes of a minimotif definition

From: A proposed syntax for Minimotif Semantics, version 1

# 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.
  1. 1 1 Attributes are broken up into 4 sections related to the Minimotif (1-6), Activity (7-9), Target (10-15), and properties (16-19) of Motif/Activity/Target minimotif sentences.