GO Terms A4 HUMAN
GOPET
First, we used GOPET to predict the GO terms of the protein.
The method only predicts functional GO terms. A4_HUMAN has 11 annotated GO functions. The methods predicts 13 GO function terms, which can be seen in Figure 1. Therefore we decided to check if all predictions are correct.
| GO term | confidence | prediction term | prediction GOid |
| endopeptidase inhibitor activity | 87% | right | wrong |
| serine-type endopeptidase inhibitor activity | 86% | right | right |
| plasmin inhibitor activity | 83% | wrong | wrong |
| trypsin inhibitor activtiy | 83% | wrong | wrong |
| peptidase inhibitor activity | 82% | right | right |
| binding | 79% | right | right |
| protein binding | 74% | right | right |
| metal ion binding | 73% | right | right |
| DNA binding | 71% | right | right |
| heparin binding | 70% | wrong | right |
| zinc ion binding | 69% | wrong | wrong |
| copper ion binding | 69% | wrong | wrong |
| iron ion binding | 67% | wrong | wrong |
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Pfam
We used the webserver for our analysis. We decided to only trust the significant Pfam-A matches. To check if the predictions are correct we mapped the Pfam ids to the Go ids with help of a mapping website [[1]]. If a successful mapping was not possible, we compared the names of the predicted Pfam family with the names of the GO terms. If the names are similar or equal, we decided to trust the mapping.
Graphical representation of the prediction result of Pfam:
Pfam found six significant Pfam-A matches:
| Family | E-Value | GOid | prediction |
| Amyloid A4 N-terminal heparin-binding | 4e-42 | none | right |
| Copper-binding of amyloid precursor CuBD | 2.3e-27 | none | right |
| Kunitz/Bovine pancreatic trypsin inhibitor domain | 3e-19 | GO:0004867 | right |
| E2 domain of amyloid precursor protein | 1.6e-74 | none | right |
| Beta-amyloid peptide (beta-APP) | 4.3e-28 | GO:0005488 | right |
| GO:0016021 | right | ||
| Beta-amyloid precursor protein C-terminus | 1.1e-29 | none | right |
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ProtFun 2.2
ProtFun 2.2 does not give clear predictions if the protein belongs to this class or not, instead it gives probabilities and odd scores.
We decided to make a cutoff by 2. So all classes with an odd score of 2 or higher are results for us. You can also find a "=>" sign in the result file. This sign shows the result with the highest information content. We also take this line as result, although if the odd score is lower than 2. If we only have result with a odd score lower than 2, the line with this sign is our onliest result.
Because the prediction categories are very general, it was not possible to map the GOids. Therefore, we checked the known GO annotations. If there was a hint for a category and the protein was predicted to be in this category, we decided that the prediction is right, otherwise if the known GO annotations and the categories conflict, we count the prediction as wrong.
The ProtFun Server calculated following prediction result for A4_HUMAN:
| Functional category | |||
|---|---|---|---|
| Functional category | Probabilty | Odd score | Prediction |
| Amino acid biosynthesis | 0.020 | 0.921 | right |
| Biosynthesis of cofactors | 0.261 | 3.623 | right |
| Cell envelope | 0.804 => | 13.186 => | right |
| Cellular processes | 0.053 | 0.070 | right |
| Central intermediary metabolism | 0.184 | 2.920 | right |
| Engergy metabolism | 0.023 | 0.259 | right |
| Fatty acid metabolsim | 0.016 | 1.265 | right |
| Purines and Pyrimidines | 0.417 | 1.716 | right |
| Regulatory functions | 0.013 | 0.084 | wrong |
| Replication and transcription | 0.029 | 0.109 | right |
| Translation | 0.027 | 0.613 | right |
| Transport and binding | 0.827 | 2.016 | right |
| Enyzme/non-enzyme | |||
| Enzyme/non-enzyme | Probability | Odd score | Prediction |
| Enzyme | 0.392 => | 1.368 => | right |
| Nonenzyme | 0.608 | 0.852 | right |
| Enyzme class | |||
| Enzyme class | Probability | Odd score | Prediction |
| Oxidoreductase (EC 1.-.-.-) | 0.024 | 0.114 | right |
| Transferase (EC 2.-.-.-) | 0.208 | 0.603 | right |
| Hydrolase (EC 3.-.-.-) | 0.190 | 0.600 | right |
| Lyase (EC 4.-.-.-) | 0.020 | 0.430 | right |
| Isomerase (EC 5.-.-.-) | 0.010 | 0.324 | right |
| Ligase (EC 6.-.-.-) | 0.048 | 0.946 | right |
| Gene ontology category | |||
| Gene ontology category | Probability | Odd score | Prediction |
| Signal transducer | 0.126 | 0.586 | right |
| Receptor | 0.036 | 0.211 | right |
| Hormone | 0.001 | 0.206 | right |
| Structural protein | 0.034 => | 1.205 => | right |
| Transporter | 0.024 | 0.222 | right |
| Ion channel | 0.009 | 0.162 | right |
| Volatge-gated ion channel | 0.002 | 0.108 | right |
| Cation channel | 0.010 | 0.215 | right |
| Transcription | 0.043 | 0.335 | right |
| Transcription regulation | 0.018 | 0.143 | right |
| Stress response | 0.076 | 0.862 | right |
| Immune response | 0.016 | 0.183 | right |
| Growth factor | 0.005 | 0.372 | right |
| Metal ion transport | 0.009 | 0.020 | right |
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