Difference between revisions of "Sequence-based predictions"
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AA: PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE<br> |
AA: PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE<br> |
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310 320 330 340<br> |
310 320 330 340<br> |
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===Jpred3=== |
===Jpred3=== |
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Revision as of 15:29, 31 May 2011
Contents
Sequence-based predictions
1. Secondary structure prediction
PSIPRED
PSIPRED HFORMAT (PSIPRED V3.0)
Conf: 999851589999999877513567886245556456636899750389988756755687
Pred: CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEECCEEEEE
AA: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF
10 20 30 40 50 60
Conf: 318998225536664688990669998865311211002358577441156788603899
Pred: ECCCCCCEEECCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCEEEE
AA: YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV
70 80 90 100 110 120
Conf: 987799319835459889765910588728988756689786135787788899999876
Pred: EEEEEEECCCEEEEEEEEEECCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
AA: ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR
130 140 150 160 170 180
Conf: 310271499889888616322000378810000468999601699981450765189996
Pred: HHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCEEEEEEEEEECCCCEEEEEE
AA: AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL
190 200 210 220 230 240
Conf: 288106667520025355899875899999965999872169986699998826885259
Pred: ECCEECCCCCCCCCCCEECCCCCEEEEEEEEECCCCCCCEEEEEECCCCCCCEEEEEECC
AA: KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS
250 260 270 280 290 300
Conf: 999711124320001367777622367764115889887620212359
Pred: CCCCCEEEEEEEEEEEEEEEEEEEEEEEEEECCCCCCCCCCEEECCCC
AA: PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
310 320 330 340
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
