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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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