Output format

DESCRIPTION For each input sequence the server predicts cellular role, enzyme class and Gene Ontology category. The scores consist of two numbers. The first number is the estimated probability that the entry belongs to the class in question. It is influenced by the prior probability of that class. The second number represents the odds that the sequence belongs to that class/category. It is independent of the prior probability. For each sequence the scores with the highest information content are marked with arrows (=>). Cellular role The input protein is classified into 12 different functional categories based on the scheme developed by Monica Riley for E. coli in 1993.
Amino acid biosynthesis Biosynthesis of cofactors Cell envelope Cellular processes Central intermediary metabolism Energy metabolism	Fatty acid metabolism Purines and pyrimidines Regulatory functions Replication and transcription Translation Transport and binding
The categories may overlap, since a protein may belong to several categories. Enzyme/nonenzyme The protein is classified as enzyme or non-enzyme:
Enzyme	Non-enzyme
Enzyme class The protein is classified into 6 different enzyme classes:
Oxidoreductase (EC 1.-.-.-) Transferase (EC 2.-.-.-) Hydrolase (EC 3.-.-.-)	Isomerase (EC 4.-.-.-) Ligase (EC 5.-.-.-) Lyase (EC 6.-.-.-)
The prediction of enzyme class is carried out even if the input protein is not predicted to be an enzyme. The purpose is to provide maximal information in borderline cases. However, no arrow marking is done for predicted non-enzymes. Gene Ontology category The prediction scores are given for the following Gene Ontology categories:
Signal transducer Receptor Hormone Structural protein Transporter Ion channel Voltage-gated ion channel	Cation channel Transcription Transcription regulation Stress response Immune response Growth factor Metal ion transport
The arrow marking is not done if the score with the highest information content has odds lower than 1. If the option "Show the individual features ... in the output" has been selected a summary of the output of the individual feature predictions used by ProtFun will be added for each input sequence (not shown here). The features include signal peptides, other localization signals and various post-translational modifications. EXAMPLE OUTPUT ############## ProtFun 2.2 predictions ############## >CIKA_HUMAN # Functional category Prob Odds Amino_acid_biosynthesis 0.011 0.500 Biosynthesis_of_cofactors 0.210 2.917 Cell_envelope 0.033 0.541 Cellular_processes 0.030 0.411 Central_intermediary_metabolism 0.048 0.762 Energy_metabolism 0.035 0.389 Fatty_acid_metabolism 0.017 1.308 Purines_and_pyrimidines 0.331 1.362 Regulatory_functions 0.034 0.211 Replication_and_transcription 0.020 0.075 Translation 0.071 1.614 Transport_and_binding => 0.773 1.885 # Enzyme/nonenzyme Prob Odds Enzyme => 0.368 1.285 Nonenzyme 0.632 0.886 # Enzyme class Prob Odds Oxidoreductase (EC 1.-.-.-) 0.048 0.231 Transferase (EC 2.-.-.-) 0.134 0.388 Hydrolase (EC 3.-.-.-) 0.075 0.237 Lyase (EC 4.-.-.-) 0.020 0.426 Isomerase (EC 5.-.-.-) 0.010 0.313 Ligase (EC 6.-.-.-) 0.032 0.629 # Gene Ontology category Prob Odds Signal_transducer 0.205 0.958 Receptor 0.007 0.041 Hormone 0.001 0.154 Structural_protein 0.003 0.107 Transporter 0.025 0.229 Ion_channel 0.169 2.965 Voltage-gated_ion_channel => 0.279 12.682 Cation_channel 0.146 3.174 Transcription 0.219 1.711 Transcription_regulation 0.111 0.888 Stress_response 0.073 0.830 Immune_response 0.011 0.129 Growth_factor 0.005 0.357 Metal_ion_transport 0.018 0.039 // >SOMA_HUMAN # Functional category Prob Odds Amino_acid_biosynthesis 0.038 1.727 Biosynthesis_of_cofactors 0.118 1.639 Cell_envelope => 0.804 13.180 Cellular_processes 0.027 0.370 Central_intermediary_metabolism 0.065 1.032 Energy_metabolism 0.035 0.389 Fatty_acid_metabolism 0.017 1.308 Purines_and_pyrimidines 0.209 0.860 Regulatory_functions 0.014 0.087 Replication_and_transcription 0.020 0.075 Translation 0.027 0.614 Transport_and_binding 0.820 2.000 # Enzyme/nonenzyme Prob Odds Enzyme 0.234 0.817 Nonenzyme => 0.766 1.073 # Enzyme class Prob Odds Oxidoreductase (EC 1.-.-.-) 0.032 0.154 Transferase (EC 2.-.-.-) 0.031 0.090 Hydrolase (EC 3.-.-.-) 0.090 0.284 Lyase (EC 4.-.-.-) 0.029 0.617 Isomerase (EC 5.-.-.-) 0.010 0.313 Ligase (EC 6.-.-.-) 0.017 0.334 # Gene Ontology category Prob Odds Signal_transducer 0.272 1.271 Receptor 0.008 0.047 Hormone => 0.114 17.538 Structural_protein 0.003 0.107 Transporter 0.043 0.394 Ion_channel 0.079 1.386 Voltage-gated_ion_channel 0.003 0.136 Cation_channel 0.010 0.217 Transcription 0.031 0.242 Transcription_regulation 0.031 0.248 Stress_response 0.223 2.534 Immune_response 0.123 1.447 Growth_factor 0.040 2.857 Metal_ion_transport 0.026 0.056 //

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