Yeast Protein Database

MIPS Yeast Database Yeast Protein Database (YPD)... 

YEPD Yeast electrophoresis protein database (YEPD)... 

Figure 1.1. Complex two-hybrid interaction networks. Two-hybrid interaction networks for proteins related to spindle pole body (A) and vesicular transport (B) are shown. Allows indicate two-hybrid interactions, beginning from the bait and ending at the prey. Double-headed allows mean that the interactions were detected bidirectionally. Note that arrows indicate the direction of two-hybrid interactions but not any biological orientation. Solid lines indicate known interactions recorded in the Yeast Proteome Database (14) but not yet detected by our two-hybrid screening [Refs in 45].

We have also downloaded the ORF data for yeast this database includes the predicted sequence of 6057 ORFs that are 100 residues or longer. Note that these data are for the full-length ORF. As result, all ORFs contain a methionine residue, which corresponds to the start codon. Post-translational proteolysis will remove the leader sequence from the N-terminus of the mature protein. Figure 21.3 presents a histogram of the abundances of each amino acid in those ORFs. The figure also reports the number of ORFs that do not contain that amino acid (no) and the percentage of all amino acids. For example, only 9 out of 6057 ORFs contain no lysine residues. The three most abundant amino acids in yeast are leucine, serine, and lysine, which account for 9.6%, 9.0%, and 7.3% of all amino acids, whereas the three least abundant amino acids are tryptophan, cysteine, and methionine, which account for 1.0%, 1.3%, and 2.1% of all amino acids the methionine abundance in mature proteins... 

A sequence tag from an unknown protein allows a number of further options for characterisation. Even a short stretch of amino acid sequence provides a powerful means of interrogating a protein database, and may provide a useful alternative to PMF in poor quality samples that may have peptides derived from more than one protein. More advanced database searching systems will find proteins with homologous sequences to that of the peptide tag. A good example of this type of database searching system is BLAST (Basic Local Alignment Sequence Tool), (Altschul et al., 1997). A modified form of this (MS BLAST) was used in conjunction with PMF to characterise the proteome of the yeast Pichia pastoris, whose genome has not been fully sequenced... 

CSH QUEST Protein Database Center (2D REF52 rat, mouse embryo, yeast. Quest software)... 

Erf2 and Akrl can thus be seen as the founding members of a family of putative PATs. In databases, over 120 DHHC-CRD genes have been found so far, with over 20 in humans. The DHHC-CRD-family of proteins contains 7 members in yeast and 23 in humans. The localization of the PATs determines where soluble proteins get stably associated to the membrane. In yeast, the DHHC proteins are widely distributed on membranes. In 2006, a global analysis of palmitoylation in yeast was performed, showing the great impact of DHHC proteins on the cellular palmitoylation events. 

To date, no mammalian factors specifically involved in ER protein degradation have been isolated. There exist entries in the sequence databases, which share similarity to the yeast Hrdl/Der3, Hrd3 and Deri proteins, respectively, however, the function of these proteins has not been determined so for. Therefore, it remains an open question whether ER protein degradation in mammalian cells requires the activity of similar cellular components that have been shown to mediate turnover of ER proteins in yeast. 

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