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HMMPFAM search against several major signature databases- PFAM, TIGRFAM, SMART, and Superfamily

What makes species different? A study of Unique Genes. Our Definition of genes with unknown function.

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HMMPFAM search against several major signature databases- PFAM, TIGRFAM, SMART, and Superfamily

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  1. What makes species different?A study of Unique Genes Our Definition of genes with unknown function Gene models and proteomes for Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Arabidopsis thaliana (At), Oryza sativa (Os), Drosophila melanogaster (Dm), Anopheles gambiae (Ag), Caenorhabditis elegans (Ce), Mus musculus (Mm), Rattus norvegicus (Rn), and Homo sapiens (Hs) were downloaded from the NCBI website (ftp.ncbi.nlm.nih.gov). HMMPFAM search against several major signature databases- PFAM, TIGRFAM, SMART, and Superfamily match to one or more of the models in any one of the databases “Known (PDF)” no matches to any one of the models in any database “Unknown(POF)”

  2. “Unknowns” account for about 25% of each genome % of Genome

  3. “Unknowns” are not as conserved as “knowns”, even between related organisms! Yeast % hits at each e-value BLAST e-value

  4. Known Unknown Sc Sp At Os Dm Ag Rn Mm Hs Ce Outl. Relationship tree among the 10 different genomes reveals a high degree of evolutionary divergence among “unknowns” from different species “Unknowns” have a different rate of evolution? “Unknowns” are new genes?

  5. 5955 1197 Known Unknown 19157 882 % Unique genes 2919 5601 3384 3173 5694 1440 836 5832 528 487 1908 2041 792 133 196 20 “Unknowns” are mainly species-specific. Representation of “unknowns” in the “unique-ome” of different species. “Unique-ome” was defined by a BLAST cut off of 10-6. Between the 10 different genomes!

  6. Known Unknown Compared to “knowns”, “Unknowns” are more disordered, less hydrophobic and shorter.

  7. “Unknown” Conclusions • Unknown genes are typically species-specific and might provide some of the keys that define species-specific differences. • Unraveling the function of “unknowns” would improve our understanding of species-specific functions. • Disordered protein functions are thought to include the formation and regulation of large multi-molecular assemblies that participate in important regulatory functions. Disordered regions on proteins have been reported to evolve significantly more rapidly than ordered regions. • “Unknowns” are likely to be the result of greater evolutionary divergence among species leading to the establishment of new, species-specific regulatory networks.

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