GO Terms LAMP1 HUMAN

GOPET

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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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:

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
Enyzme/non-enzyme
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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