Difference between revisions of "Fabry:Sequence-based analyses"
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== Signal peptides == |
== Signal peptides == |
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| − | + | Prediction of the presence and location of signal peptide cleavage sites in amino acid sequences. |
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| − | === α-Galactosidase A (P06280) === |
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| − | <figure id="fig:1r46_SP"> [[File:FABRY_sp_P06280_AGAL_HUMAN.png|right|350px|thumb|<caption>Human α-Galactosidase A, plot of scores for signal peptide cleavage site ([http://www.cbs.dtu.dk/services/SignalP/ source])</caption>]] </figure> |
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| − | '''organism:''' Homo sapiens (Human)<br> |
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| − | '''pdb-id:''' 1r46<br> |
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| − | '''Signal-peptide:''' 1-31<br> |
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| − | '''Signal-peptide sequence:''' MQLRNPELHLGCALALRFLALVSWDIPGARAL<br> |
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| − | As already described in section [[Fabry:Sequence-based_analyses#.CE.B1-Galactosidase_A_.28P06280.29 | Transmembrane helices]] the human α-Galactosidase A does not have transmembrane helical structures and from our background knowledge we know that the protein has a 31 residues long signal peptide at the N-terminus. The protein's pdb structure is available only without signal peptide, since those residues are cleaved off. Therefore no picture is provided here.<br> |
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| − | In <xr id="fig:1r46_SP"/> the signal peptide prediction of SignalP 4.0 is shown. The cleaved site is clearly indicated after residue 31, since the S-score (green) drops and the C- (red) and Y-score (blue) not only have a peak at this position, but attain their maximum at this point ([https://www.dropbox.com/s/ptsu877rv5tq0h7/sp_P06280_AGAL_HUMAN.sigp.txt see SignalP output file] ) |
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| − | <br style="clear:both;"> |
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| − | === Serum Albumin (P02768) === |
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| − | '''organism:''' Homo sapiens (Human)<br> |
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| − | '''pdb-id:''' 1ao6<br> |
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| − | '''Signal-peptide:''' 1-18<br> |
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| − | '''Signal-peptide sequence:''' MKWVTFISLLFLFSSAYS<br> |
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| − | <br style="clear:both;"> |
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| − | === Lysosome-associated membrane glycoprotein 1 (P11279) === |
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| − | '''organism:''' Homo sapiens (Human)<br> |
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| − | '''pdb-id:''' na<br> |
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| − | '''Signal-peptide:''' 1-28<br> |
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| − | '''Signal-peptide sequence:''' MAAPGSARRPLLLLLLLLLLGLMHCASA<br> |
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| − | <br style="clear:both;"> |
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| − | === Aquaporin-4 (P47863) === |
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| − | '''organism:''' Rattus norvegicus (Rat)<br> |
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| − | '''pdb-id:''' 2d57<br> |
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| − | '''Signal-peptide:''' none<br> |
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| − | '''Signal-peptide sequence:''' ---<br> |
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| − | <br style="clear:both;"> |
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== GO terms == |
== GO terms == |
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Revision as of 15:12, 12 May 2012
Fabry Disease » Sequence-based analyses
The following analyses were performed on the basis of the α-Galactosidase A sequence. Please consult the journal for the commands used to generate the results.
Contents
Secondary structure
Disorder
Transmembrane helices
α-Galactosidase A (P06280)
Aquaporin-4 (P47863)
Signal peptides
Prediction of the presence and location of signal peptide cleavage sites in amino acid sequences.
GO terms
GOPET
Searching the GOPET annotation tool with the AGAL_HUMAN sequence revealed 5 GOIds, which are displayed in <xr id="tab:GOPET"/>. On a first glance, since we already know the name and function of the protein, it is a bit surprising, that alpha-galactosidase activity is only the third entry with 96% confidence. In our already carried out information gathering we learned that α-galactosidase A is a hydrolase thus the first three entries were not surprising. Considering that our enzyme mainly is a glycosidase, the both entries on top of the list make perfekt sense.
Again a bit surprising was the last entry. α-N-Acetylgalactosaminidase is actually used for enzyme replacement therapy, which we mention on our main page. The structure of both enzymes is similar to each other, but this still does not explain the association of this GO term to the AGAL protein.
<figtable id="tab:GOPET"> The results of the GOPET search
| Result for GOPET search | |||||
|---|---|---|---|---|---|
| GOid | Aspect | Confidence | GO term | ||
| GO:0016798 | Molecular Function Ontology (F) | 98% | hydrolase activity acting on glycosyl bonds | ||
| GO:0004553 | Molecular Function Ontology (F) | 98% | hydrolase activity hydrolyzing O-glycosyl compounds | ||
| GO:0016787 | Molecular Function Ontology (F) | 97% | hydrolase activity | ||
| GO:0004557 | Molecular Function Ontology (F) | 96% | alpha-galactosidase activity | ||
| GO:0008456 | Molecular Function Ontology (F) | 89% | alpha-N-acetylgalactosaminidase activity | ||
</figtable>
ProtFun2.0
EC=3.2.1.22(EC 3.-.-.- Hydrolase)
Predicted: EC 6.-.-.-(Ligase)
############## ProtFun 2.2 predictions ############## >gi_4504009_ # Functional category Prob Odds Amino_acid_biosynthesis 0.283 12.847 Biosynthesis_of_cofactors 0.339 4.708 Cell_envelope => 0.652 10.690 Cellular_processes 0.057 0.783 Central_intermediary_metabolism 0.400 6.343 Energy_metabolism 0.151 1.678 Fatty_acid_metabolism 0.032 2.448 Purines_and_pyrimidines 0.506 2.082 Regulatory_functions 0.013 0.083 Replication_and_transcription 0.047 0.175 Translation 0.211 4.807 Transport_and_binding 0.549 1.339 # Enzyme/nonenzyme Prob Odds Enzyme => 0.805 2.811 Nonenzyme 0.195 0.273 # Enzyme class Prob Odds Oxidoreductase (EC 1.-.-.-) 0.176 0.845 Transferase (EC 2.-.-.-) 0.195 0.564 Hydrolase (EC 3.-.-.-) 0.244 0.769 Lyase (EC 4.-.-.-) 0.029 0.608 Isomerase (EC 5.-.-.-) 0.010 0.321 Ligase (EC 6.-.-.-) => 0.141 2.776 # Gene Ontology category Prob Odds Signal_transducer 0.090 0.419 Receptor 0.014 0.083 Hormone 0.002 0.318 Structural_protein 0.004 0.127 Transporter 0.024 0.222 Ion_channel 0.010 0.169 Voltage-gated_ion_channel 0.003 0.127 Cation_channel 0.010 0.215 Transcription 0.047 0.367 Transcription_regulation 0.026 0.204 Stress_response 0.049 0.552 Immune_response 0.012 0.136 Growth_factor 0.006 0.412 Metal_ion_transport 0.009 0.020 //
