Protein Sequence Database Curation

We used three online protein sequence databases to create our protein datasets: Uniprot KB, UniprotKB/Swissprot, and NCBI Entrez-Protein. UniprotKB (www.uniprot.org) is an online repository of protein sequences; UniprotKB/Swissprot (http://ca.expasy.org/sprot/) builds upon this repository through annotation of protein sequences. Information available in UniprotKB/Swissprot includes citations for related publications, species name, protein family, domain structure and detail on protein variants and structure. NCBI Entrez-Protein (http://www.ncbi.nlm.nih.gov/protein/) is an online protein sequence database curated by the National Center for Biotechnology Information (NCBI).
The protein kinase C dataset of 127 protein sequences was downloaded from the NCBI Entrez-Protein and UniProtKB/SwissProt databases. The hemoglobin and myoglobin datasets, of 904 and 150 protein sequences respectively, were downloaded from the UniProtKB database. In order to ensure that sequences were not fragments or labeled incorrectly by protein family, sequences were analyzed using the SMART domain recognition software on the UniProtKB website. In addition, for all sequences the family classification was confirmed and the subfamily classification was assigned based on peer-reviewed journal articles which were obtained through the SwissProt database reference listings and based on notations on the UniProtKB entries where detailed information from articles was not available.