Difference between revisions of "Sequence-based predictions"
From Bioinformatikpedia
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===PSIPRED=== |
===PSIPRED=== |
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<code> |
<code> |
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| + | PSIPRED HFORMAT (PSIPRED V3.0) |
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| − | Conf: Confidence 0 =low 9 =high |
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| + | Conf: 999851589999999877513567886245556456636899750389988756755687<br> |
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| − | Pred: Predicted secondary structure H =helix E =strand C =coil |
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| + | Pred: CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEECCEEEEE<br> |
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| − | AA: Target sequence |
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| + | AA: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF<br> |
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| − | C o n f : 9 9 9 8 5 1 5 8 9 9 9 9 9 9 9 8 7 7 5 1 3 5 6 7 8 8 6 2 4 5 5 5 6 4 5 6 6 3 6 8 9 9 7 5 0 3 8 9 9 8 8 7 5 6 7 5 5 6 8 7 |
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| + | 10 20 30 40 50 60<br> |
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| − | P r e d : C C C C C H H H H H H H H H H H H H H H C C C C C C C E E E E E E E E E E E C C C C C C C E E E E E E E E C C E E E E E |
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| + | Conf: 318998225536664688990669998865311211002358577441156788603899<br> |
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| − | A A : M G P R A R P A L L L L M L L Q T A V L Q G R L L R S H S L H Y L F M G A S E Q D L G L S L F E A L G Y V D D Q L F V F |
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| + | Pred: ECCCCCCEEECCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCEEEE<br> |
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| − | 1 0 2 0 3 0 4 0 5 0 6 0 |
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| + | AA: YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV<br> |
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| − | C o n f : 3 1 8 9 9 8 2 2 5 5 3 6 6 6 4 6 8 8 9 9 0 6 6 9 9 9 8 8 6 5 3 1 1 2 1 1 0 0 2 3 5 8 5 7 7 4 4 1 1 5 6 7 8 8 6 0 3 8 9 9 |
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| + | 70 80 90 100 110 120<br> |
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| − | P r e d : E C C C C C C E E E C C C C C C C C C C H H H H H H H H H H H H C C C C C H H H H H H H H H H H C C C C C C C C E E E E |
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| + | Conf: 987799319835459889765910588728988756689786135787788899999876<br> |
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| − | A A : Y D H E S R R V E P R T P W V S S R I S S Q M W L Q L S Q S L K G W D H M F T V D F W T I M E N H N H S K E S H T L Q V |
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| + | Pred: EEEEEEECCCEEEEEEEEEECCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH<br> |
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| − | 7 0 8 0 9 0 1 0 0 1 1 0 1 2 0 |
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| + | AA: ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR<br> |
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| − | C o n f : 9 8 7 7 9 9 3 1 9 8 3 5 4 5 9 8 8 9 7 6 5 9 1 0 5 8 8 7 2 8 9 8 8 7 5 6 6 8 9 7 8 6 1 3 5 7 8 7 7 8 8 8 9 9 9 9 9 8 7 6 |
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| + | 130 140 150 160 170 180<br> |
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| − | P r e d : E E E E E E E C C C E E E E E E E E E E C C C E E E E E C C C C C C C C C C C C C C H H H H H H H H H H H H H H H H H H |
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| + | Conf: 310271499889888616322000378810000468999601699981450765189996<br> |
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| − | A A : I L G C E M Q E D N S T E G Y W K Y G Y D G Q D H L E F C P D T L D W R A A E P R A W P T K L E W E R H K I R A R Q N R |
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| + | Pred: HHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCEEEEEEEEEECCCCEEEEEE<br> |
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| − | 1 3 0 1 4 0 1 5 0 1 6 0 1 7 0 1 8 0 |
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| + | AA: AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL<br> |
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| − | C o n f : 3 1 0 2 7 1 4 9 9 8 8 9 8 8 8 6 1 6 3 2 2 0 0 0 3 7 8 8 1 0 0 0 0 4 6 8 9 9 9 6 0 1 6 9 9 9 8 1 4 5 0 7 6 5 1 8 9 9 9 6 |
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| + | 190 200 210 220 230 240<br> |
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| − | P r e d : H H H C C C H H H H H H H H H H C C C C C C C C C C C C C E E E E C C C C C C C E E E E E E E E E E C C C C E E E E E E |
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| + | Conf: 288106667520025355899875899999965999872169986699998826885259<br> |
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| − | A A : A Y L E R D C P A Q L Q Q L L E L G R G V L D Q Q V P P L V K V T H H V T S S V T T L R C R A L N Y Y P Q N I T M K W L |
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| + | Pred: ECCEECCCCCCCCCCCEECCCCCEEEEEEEEECCCCCCCEEEEEECCCCCCCEEEEEECC<br> |
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| − | 1 9 0 2 0 0 2 1 0 2 2 0 2 3 0 2 4 0 |
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| + | AA: KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS<br> |
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| − | C o n f : 2 8 8 1 0 6 6 6 7 5 2 0 0 2 5 3 5 5 8 9 9 8 7 5 8 9 9 9 9 9 9 6 5 9 9 9 8 7 2 1 6 9 9 8 6 6 9 9 9 9 8 8 2 6 8 8 5 2 5 9 |
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| + | 250 260 270 280 290 300<br> |
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| − | P r e d : E C C E E C C C C C C C C C C C E E C C C C C E E E E E E E E E C C C C C C C E E E E E E C C C C C C C E E E E E E C C |
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| − | A A : K D K Q P M D A K E F E P K D V L P N G D G T Y Q G W I T L A V P P G E E Q R Y T C Q V E H P G L D Q P L I V I W E P S |
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| − | 2 5 0 2 6 0 2 7 0 2 8 0 2 9 0 3 0 0 |
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| − | C o n f : 9 9 9 7 1 1 1 2 4 3 2 0 0 0 1 3 6 7 7 7 7 6 2 2 3 6 7 7 6 4 1 1 5 8 8 9 8 8 7 6 2 0 2 1 2 3 5 9 |
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| − | P r e d : C C C C C E E E E E E E E E E E E E E E E E E E E E E E E E E C C C C C C C C C C E E E C C C C |
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| − | A A : P S G T L V I G V I S G I A V F V V I L F I G I L F I I L R K R Q G S R G A M G H Y V L A E R E |
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</code> |
</code> |
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| + | |||
| + | |||
| + | Conf: 999711124320001367777622367764115889887620212359 |
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| + | |||
| + | Pred: CCCCCEEEEEEEEEEEEEEEEEEEEEEEEEECCCCCCCCCCEEECCCC |
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| + | |||
| + | AA: PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE |
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| + | |||
| + | 310 320 330 340 |
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===Jpred3=== |
===Jpred3=== |
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Revision as of 15:28, 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
