Difference between revisions of "Sequence-based mutation analysis GLA"
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=Mutation Analysis= |
=Mutation Analysis= |
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+ | ==Physicochemical Properties and Changes== |
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+ | ==Substitution Matrices== |
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+ | ===BLOSUM62=== |
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+ | ===PAM(1/250)=== |
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+ | ==PSSM== |
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+ | ==Multiple Sequence Alignment== |
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+ | ==Secondary Structure== |
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+ | ==Programs== |
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+ | ===SNAP=== |
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+ | ===SIFT=== |
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+ | ===PolyPhen=== |
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=Discussion= |
=Discussion= |
Revision as of 19:29, 27 June 2011
by Benjamin Drexler and Fabian Grandke
Contents
Introduction
Selected Mutations
We randomly selected ten annotated point mutations of the human gene GLA and they were chosen out of a pool of mutations that consist of two subsets. The first subset contains mutations that are present in HGMD and these mutations were already gathered in the task 4 Mapping SNPs. The second subset are mutations that are present in dbSNP, but not included in HGMD. This was only the case for three mutations.
Mutations at the amino acid position between 1 and 31 were not included in the selection process, because they are part of the signal peptide (see UniProt entry) and they are not present in the reference structure (PDB ID 1R47).
Number | AA-Position | Codon change | Amino acid change | Visualization |
---|---|---|---|---|
1 | 42 | ATG-ACG | Met -> Thr | |
2 | 65 | AGT-ACG | Ser -> Thr | |
3 | 117 | ATT-AGT | Ile -> Ser | |
4 | 143 | cGCA-ACA | Ala -> Thr | |
5 | 186 | CAC-CGC | His -> Arg | |
6 | 205 | gCCT-ACT | Pro -> Thr | |
7 | 244 | gGAC-CAC | Asp -> His | |
8 | 283 | CAG-CCG | Gln -> Pro | |
9 | 321 | tCAG-TAG | Gln -> Glu | |
10 | 363 | TATa-TAA | Tyr -> Cys |
The visualization was done by using PyMol and the mutagensis of the residue was performed according to this tutorial. The residue of the wildtype is colored green and the mutated residue is colored red.