Revision as of 15:52, 31 May 2011

Sequence-based predictions

1. Secondary structure prediction

PSIPRED

Jpred3

Comparison with DSSP

2. Prediction of disordered regions

DISOPRED

POODLE

IUPRED

3. Prediction of transmembrane alpha-helices and signal peptides

TMHMM

Phobius and PolyPhobius

OCTOPUS and SPOCTOPUS

SignalP

TargetP

4. Prediction of GO terms

Generel

HFE is annotated with 27 different GO Terms which are <ref>http://www.ebi.ac.uk/QuickGO/GProtein?ac=Q30201</ref>:

GOID	GO Term	Aspect
GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	Process
GO:0005515	protein binding	Function
GO:0005737	cytoplasm	Component
GO:0005769	early endosome	Component
GO:0005886	plasma membrane	Component
GO:0005887	integral to plasma membrane	Component
GO:0006461	protein complex assembly	Process
GO:0006810	transport	Process
GO:0006811	ion transport	Process
GO:0006826	iron ion transport	Process
GO:0006879	cellular iron ion homeostasis	Process
GO:0006898	receptor-mediated endocytosis	Process
GO:0006955	immune response	Process
GO:0007565	female pregnancy	Process
GO:0010106	cellular response to iron ion starvation	Process
GO:0016020	membrane	Component
GO:0016021	integral to membrane	Component
GO:0019882	antigen processing and presentation	Process
GO:0031410	cytoplasmic vesicle	Component
GO:0042446	hormone biosynthetic process	Process
GO:0042612	MHC class I protein complex	Component
GO:0045177	apical part of cell	Component
GO:0045178	basal part of cell	Component
GO:0048471	perinuclear region of cytoplasm	Component
GO:0055037	recycling endosome	Component
GO:0055072	iron ion homeostasis	Process
GO:0060586	multicellular organismal iron ion homeostasis	Process

GOPET

Gopet predicted 2 GO-Terms which have no overlab to the annotation.

GOID	Aspect	Confidence	GO Term
GO:0004872	Molecular Function	91%	receptor activity
GO:0030106	Molecular Function	88%	MHC class I receptor activity

Pfam

ProtFun 2.2

Functional category Prob Odds

 Amino_acid_biosynthesis              0.011    0.484
 Biosynthesis_of_cofactors            0.105    1.452
 Cell_envelope                     => 0.633   10.377
 Cellular_processes                   0.095    1.297
 Central_intermediary_metabolism      0.231    3.663
 Energy_metabolism                    0.059    0.659
 Fatty_acid_metabolism                0.016    1.265
 Purines_and_pyrimidines              0.583    2.400
 Regulatory_functions                 0.013    0.079
 Replication_and_transcription        0.019    0.073
 Translation                          0.079    1.801
 Transport_and_binding                0.732    1.785

Enzyme/nonenzyme Prob Odds

 Enzyme                               0.208    0.727
 Nonenzyme                         => 0.792    1.110

Enzyme class Prob Odds

 Oxidoreductase (EC 1.-.-.-)          0.084    0.404
 Transferase    (EC 2.-.-.-)          0.062    0.179
 Hydrolase      (EC 3.-.-.-)          0.135    0.425
 Lyase          (EC 4.-.-.-)          0.049    1.054
 Isomerase      (EC 5.-.-.-)          0.010    0.321
 Ligase         (EC 6.-.-.-)          0.042    0.827

Gene Ontology category Prob Odds

 Signal_transducer                    0.201    0.939
 Receptor                             0.353    2.076
 Hormone                              0.002    0.365
 Structural_protein                   0.005    0.190
 Transporter                          0.024    0.219
 Ion_channel                          0.008    0.147
 Voltage-gated_ion_channel            0.002    0.085
 Cation_channel                       0.010    0.221
 Transcription                        0.036    0.283
 Transcription_regulation             0.018    0.147
 Stress_response                      0.274    3.108
 Immune_response                   => 0.381    4.486
 Growth_factor                        0.013    0.943
 Metal_ion_transport                  0.009    0.02

Difference between revisions of "Sequence-based predictions"