From Bioinformatikpedia


First, we predict the GO terms with GOPET.

Figure 1: Result of the GOPET prediction for LAMP1_HUMAN

The method only predicts functional GO terms. LAMP1_HUMAN has 0 annotated GO functions. The methods predicts 2 GO function terms, which can be seen on Figure 1. Therefore the predictions are wrong.
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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:

Figure 2: Result of the Pfam prediction for LAMP1_HUMAN

Pfam found one significant Pfam-A matches:

Family E-Value GOid prediction
Lysosome-associated membrane glyoprotein (LAMP) 2.3e-135 GO:0016020 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 LAMP1_HUMAN:

Functional category
Functional category Probability Odd score Prediction
Amino acid biosynthesis 0.011 0.484 right
Biosynthesis of cofactors 0.053 0.735 right
Cell envelope 0.804 => 13.186 => right
Cellular processes 0.027 0.373 right
Central intermediary metabolism 0.138 2.188 right
Engergy metabolism 0.037 0.411 right
Fatty acid metabolsim 0.016 1.265 right
Purines and Pyrimidines 0.533 2.195 wrong
Regulatory functions 0.015 0.090 right
Replication and transcription 0.019 0.073 right
Translation 0.027 0.613 right
Transport and binding 0.834 2.033 right
Enzyme/non-enzyme Probability Odd score Prediction
Enzyme 0.276 0.965 right
Nonenzyme 0.724 => 1.014 => right
Enyzme class
Enzyme class Probability Odd score Prediction
Oxidoreductase (EC 1.-.-.-) 0.039 0.187 right
Transferase (EC 2.-.-.-) 0.046 0.134 right
Hydrolase (EC 3.-.-.-) 0.058 0.184 right
Lyase (EC 4.-.-.-) 0.020 0.430 right
Isomerase (EC 5.-.-.-) 0.010 0.321 right
Ligase (EC 6.-.-.-) 0.017 0.326 right
Gene ontology category
Gene ontology category Probability Odd score Prediction
Signal transducer 0.396 1.849 right
Receptor 0.282 1.659 right
Hormone 0.001 0.206 right
Structural protein 0.011 0.408 right
Transporter 0.024 0.222 right
Ion channel 0.008 0.147 right
Volatge-gated ion channel 0.002 0.111 right
Cation channel 0.010 0.215 right
Transcription 0.032 0.247 right
Transcription regulation 0.018 0.142 right
Stress response 0.246 2.795 right
Immune response 0.371 => 4.368 => right
Growth factor 0.013 0.956 right
Metal ion transport 0.009 0.020 right

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