LOC56985 results: Difference between revisions
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[[Image:Dali results.png|right|thumb|400px|Figure 1: Table showing the top 20 structural homologs of the ''Danio rerio'' gene ortholog. Match 1 is the ''Danio rerio'' protein (2nxf-A); 2dxl-A is a phosphorhydrolase from ''Enterbacter aerogenes'', followed by purple acid phosphatases from human (1war-A), Norwegian rat (1qhw-A) and pig (1ute-A). The remainder of the top homologs shown here are predominantly from Kidney Bean(''Phaseolus vulgaris'') purple acid phosphatase, which are assigned either 1kbp, 3kbp and 4kbp. This protein is a mutimer and has therefore returned results from all of its chains (designated A to D) ]]A structural comparison search of the ''Danio rerio'' ortholog (2nxf) showed that the gene product had its greatest similarity to a phosphorhydrolase and to various purple acid phosphatases (figure 1). All of these protein matches showed little sequence similarity to the 2nxf however the Z-score of these proteins were significant based on the guide given on the Dali server that Z-scores below 2.5 are insignificant matches. The top hit, 2dxl-A, showed a Z-score of 24.1; other members in the top five matches again showed Z-scores of above 20. Dali works by fitting the two structures together and determining how far apart each of the atoms are from one another to give a root mean square deviation (rmsd), even in the lowest of the top 20 matches the rmsd is 3.0 or below. | |||
[[LOC56985_abstract| Abstract]] | [[LOC56985_intro| Introduction]] | [[LOC56985_results| Results]] | [[LOC56985_discussion| Discussion]] | | [[LOC56985_abstract| Abstract]] | [[LOC56985_intro| Introduction]] | [[LOC56985_results| Results]] | [[LOC56985_discussion| Discussion]] | | ||
Revision as of 00:53, 31 May 2008
A structural comparison search of the Danio rerio ortholog (2nxf) showed that the gene product had its greatest similarity to a phosphorhydrolase and to various purple acid phosphatases (figure 1). All of these protein matches showed little sequence similarity to the 2nxf however the Z-score of these proteins were significant based on the guide given on the Dali server that Z-scores below 2.5 are insignificant matches. The top hit, 2dxl-A, showed a Z-score of 24.1; other members in the top five matches again showed Z-scores of above 20. Dali works by fitting the two structures together and determining how far apart each of the atoms are from one another to give a root mean square deviation (rmsd), even in the lowest of the top 20 matches the rmsd is 3.0 or below.
Abstract | Introduction | Results | Discussion | Conclusion | Method | References
