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The CGD Protein Physicochemical Properties Page displays a number of properties and statistics calculated directly from the predicted ORF translation, assuming no post-translational processing or modification. This is an unrealistic assumption for most proteins, and users requiring accurate values for these properties should consult the literature for experimentally derived values. Nevertheless, the values may serve as a helpful snapshot, giving the user a general idea of the physicochemical nature of the subject protein.
Property values are calculated locally, making use of several methods from ExPASy's ProtParam tool. Codon usage statistics are also computed locally, using the CodonW program.
The top of the page provides a site-wide quick search, links to the major CGD informational resources, and a bar with links to popular tools, such as a local BLAST search. Beneath this is a series of tabs linking to other locus-specific information pages, including Locus Summary, Locus History, Literature, Gene Ontology, and Phenotype.
The number and compositional percentage (100 x NumberAA/protein length) of each standard amino acid (AA).
Estimated using the method of Pace et al., which calculates the sum of (NumberAA x Extinction CoefficientAA) for three amino acids that absorb at 280 nm: tyrosine, tryptophan, and the dimeric amino acid cystine (two cysteine [Cys] residues covalently joined through a disulfide bond). Two extinction coefficients are displayed:
The absorbance of the protein at 280 nm (A280, or OD280) is calculated by dividing the extinction coefficient by the molecular weight of the protein.
The codon usage indices below tend to correlate with gene expression levels. Very low index values may indicate an incorrect gene model. See the CodonW Indices note for more information.
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