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+ | [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/images/3/33/Fabry_disease_mutation_analysis_sequence_msa_100.png Multiple sequence alignment of 100 sequences by T-Coffee in JalView.] |
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Revision as of 03:40, 28 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.
Mutation Analysis
Physicochemical Properties and Changes
Substitution Matrices
BLOSUM62 | PAM1 | PAM250 | |||||
---|---|---|---|---|---|---|---|
Number | Substitution | Mutation | Worst | Mutation | Worst | Mutation | Worst |
1 | Met -> Thr | -1 | -3 | 2 | 0 | 1 | 0 |
2 | Ser -> Thr | 1 | -3 | 38 | 0 | 9 | 3 |
3 | Ile -> Ser | -2 | -4 | 1 | 0 | 3 | 1 |
4 | Ala -> Thr | -1 | -3 | 32 | 0 | 11 | 2 |
5 | His -> Arg | 0 | -3 | 8 | 0 | 5 | 2 |
6 | Pro -> Thr | 1 | -4 | 4 | 0 | 5 | 1 |
7 | Asp -> His | -1 | -4 | 4 | 0 | 6 | 1 |
8 | Gln -> Pro | -1 | -3 | 6 | 0 | 4 | 1 |
9 | Gln -> Glu | 2 | -3 | 27 | 0 | 7 | 1 |
10 | Arg -> Cys | -3 | -3 | 1 | 0 | 2 | 1 |
PSSM
Number | Amino acid | A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V | A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
42 | M | -3 | -2 | -5 | -6 | -4 | -3 | -5 | -6 | -5 | 1 | 1 | -4 | 9 | -1 | -5 | -4 | -3 | -5 | -4 | 2 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 12 | 1 | 58 | 2 | 0 | 0 | 1 | 0 | 0 | 15 | 1.55 | 1.56 | |
65 | S | -2 | -1 | 5 | -1 | -3 | -2 | -2 | -2 | -1 | -3 | -3 | -1 | -3 | 0 | -2 | 3 | 3 | 0 | -1 | -3 | 2 | 2 | 28 | 3 | 0 | 1 | 2 | 2 | 1 | 1 | 2 | 3 | 0 | 4 | 2 | 20 | 20 | 1 | 2 | 1 | 0.59 | 1.27 | |
117 | I | -4 | -5 | -5 | -6 | -4 | -4 | -5 | -5 | -5 | 4 | 4 | -5 | 5 | 3 | -2 | -3 | -4 | 1 | -1 | -1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 25 | 35 | 0 | 17 | 11 | 2 | 2 | 0 | 2 | 2 | 1 | 0.93 | 1.42 | |
143 | A | 1 | 1 | 0 | 2 | 1 | 0 | -1 | 0 | 2 | -1 | -2 | -1 | 2 | 0 | 1 | -1 | -1 | -5 | 0 | -1 | 14 | 7 | 4 | 11 | 3 | 5 | 5 | 6 | 5 | 3 | 4 | 3 | 5 | 5 | 6 | 4 | 4 | 0 | 3 | 3 | 0.12 | 1.86 | |
186 | H | 2 | 1 | 1 | -1 | -5 | 1 | 1 | -2 | 0 | -1 | -1 | 0 | 1 | -1 | 1 | -2 | -1 | -5 | 1 | -1 | 17 | 9 | 6 | 3 | 0 | 7 | 9 | 3 | 3 | 3 | 5 | 5 | 3 | 2 | 8 | 3 | 4 | 0 | 6 | 5 | 0.16 | 1.91 | |
205 | P | -1 | -2 | 1 | 1 | -5 | -1 | 2 | 3 | 1 | -5 | -2 | -2 | -4 | -1 | 2 | 0 | -2 | -5 | -1 | -4 | 6 | 2 | 7 | 7 | 0 | 2 | 14 | 24 | 4 | 0 | 5 | 2 | 0 | 3 | 12 | 7 | 2 | 0 | 2 | 1 | 0.38 | 1.69 | |
244 | D | -2 | -2 | 3 | 4 | 0 | -2 | 0 | 0 | 1 | 0 | -1 | -1 | 1 | -3 | 0 | -1 | -1 | -5 | 1 | -2 | 3 | 2 | 13 | 23 | 2 | 2 | 5 | 7 | 3 | 6 | 5 | 4 | 3 | 1 | 6 | 4 | 3 | 0 | 6 | 3 | 0.31 | 1.95 | |
283 | Q | -2 | 2 | -2 | -3 | -5 | 3 | -2 | -4 | 8 | -2 | -1 | -2 | 1 | -3 | -5 | -2 | -2 | 0 | -1 | -1 | 4 | 11 | 1 | 1 | 0 | 15 | 2 | 1 | 37 | 2 | 8 | 2 | 4 | 1 | 0 | 2 | 3 | 1 | 2 | 4 | 0.96 | 1.70 | |
321 | Q | -2 | 1 | -2 | -2 | -5 | 7 | 1 | -4 | -2 | -4 | -3 | 1 | -2 | -5 | -3 | -2 | -3 | 1 | -3 | -4 | 2 | 6 | 1 | 1 | 0 | 62 | 7 | 1 | 1 | 1 | 2 | 8 | 1 | 0 | 1 | 2 | 1 | 2 | 1 | 1 | 1.29 | 1.54 | |
363 | R | 0 | 2 | -2 | -3 | -1 | 3 | -1 | -4 | -1 | 1 | 0 | -1 | 3 | 0 | -3 | 0 | -1 | -4 | 2 | 1 | 7 | 13 | 1 | 1 | 1 | 12 | 4 | 1 | 1 | 8 | 7 | 4 | 6 | 3 | 1 | 6 | 4 | 0 | 7 | 11 | 0.24 | 1.6 |
Multiple Sequence Alignment
Multiple sequence alignment of 100 sequences by T-Coffee in JalView.
Number | Position | Conservation all (Jalview) | Conservation best 25 (Jalview) |
---|---|---|---|
1 | 42 | 10 | 11 |
2 | 65 | 8 | 11 |
3 | 117 | 9 | 9 |
4 | 143 | 10 | 8 |
5 | 186 | 4 | 2 |
6 | 205 | 10 | 11 |
7 | 244 | 10 | 11 |
8 | 283 | 11 | 11 |
9 | 321 | 11 | 11 |
10 | 363 | 3 | 5 |
A table of the sequences is provided on this page.