Identification of DNA binding proteins and most abundant proteins in PBCV-1 virion from MALDI-TOF PMF analysis.

The table lists (in bold) the PBCV-1 CDSs from which peptides were detected in MALDI-TOF spectra. The peptides correspond to DNA associated proteins described in Fig. 3. Only database entries with a protein score with a significance <0.05 are presented. The identity of the A278L protein was confirmed by the MS/MS sequencing of 3 peptides. Also included are the copy numbers per virion of the most abundant proteins in PBCV-1 virion. The copy numbers were estimated using the exponentially modified protein abundance index (emPAI) algorithm [40]. Based on the knowledge that the major capsid protein (A430L) is present in 1440 copies per virion, we calculated the abundances of the major proteins in the virion. For these proteins, parameters such as the molecular weight (MW), the isoelectric point (IP) and the functional annotation from the Greengene database (http://greengene.uml.edu/database/php/get_orf.php?genome_name=PBCV1) are provided. Putative DNA binding sites were further identified by the BindN algorithm (http://bioinfo.ggc.org/bindn). The data are presented as percentage of putative DNA binding sites relative to total protein (% DNA binding).