Difference between revisions of "Sequence-based predictions"
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'''Prediction''' of disordered residiues |
'''Prediction''' of disordered residiues |
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Number Residue NORSnet NORS2st PROFbval bval2st Ucon Ucon2st MD_raw MD_rel MD2st |
Number Residue NORSnet NORS2st PROFbval bval2st Ucon Ucon2st MD_raw MD_rel MD2st |
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348 E 0.34 - 0.92 D 0.38 - 0.520 0 D |
348 E 0.34 - 0.92 D 0.38 - 0.520 0 D |
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+ | Key for output |
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+ | ---------------- |
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− | Key for output |
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+ | Number - residue number |
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− | ---------------- |
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+ | Residue - amino-acid type |
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− | Number - residue number |
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+ | NORSnet - raw score by NORSnet (prediction of unstructured loops) |
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− | Residue - amino-acid type |
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− | + | NORS2st - two-state prediction by NORSnet; D=disordered |
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+ | PROFbval - raw score by PROFbval (prediction of residue flexibility from sequence) |
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− | NORS2st - two-state prediction by NORSnet; D=disordered |
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+ | Bval2st - two-state prediction by PROFbval |
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− | PROFbval - raw score by PROFbval (prediction of residue flexibility from sequence) |
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+ | Ucon - raw score by Ucon (prediction of protein disorder using predicted internal contacts) |
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− | Bval2st - two-state prediction by PROFbval |
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+ | Ucon2st - two-state prediction by Ucon |
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− | Ucon - raw score by Ucon (prediction of protein disorder using predicted internal contacts) |
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+ | MD - raw score by MD (prediction of protein disorder using orthogonal sources) |
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− | Ucon2st - two-state prediction by Ucon |
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+ | MD_rel - reliability of the prediction by MD; values range from 0-9. 9=strong prediction |
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− | MD - raw score by MD (prediction of protein disorder using orthogonal sources) |
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− | + | MD2st - two-state prediction by MD |
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− | MD2st - two-state prediction by MD |
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=Prediction of transmembrane alpha-helices and signal peptides= |
=Prediction of transmembrane alpha-helices and signal peptides= |
Revision as of 19:11, 10 June 2011
Contents
Secondary structure prediction
PSIPRED
PSI-PRED use the PSI-BLAST output as input for a neuronal network which has a single hidden layer and a feed-forward back-propagation architecture to predict the secondary structure. PSI-PRED predicts a alpha/beta structure. The transmembrane region is predicted as a beta region.
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
Jpred uses the Jnet algorithm which provides "a three-state (a-helix, ß-strand and coil) prediction of secondary structure at an accuracy of 81.5%" <ref>http://nar.oxfordjournals.org/content/36/suppl_2/W197.abstract</ref>.
Jpred found in it's first blast search a lot of homologous hits with an e-value range from e-163 to 4e-44. There are some self hits included. We continued to the prediction which is:
Seq: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDD SS: ------HHHHHHHHHHHHH---------EEEEEEEEE-------EEEEEEEEE-- Seq: QLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHN SS: EEEEEE-----EEEE----------HHHHHHHHHHHHHHHHHHHHHHHHHH---- Seq: HSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPT SS: -----EEEEEEEEEE------EEEEEEE-----EEEEEE----EEE-------HH Seq: KLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSV SS: HHHHH--HHHHHHHHHH------HHHHHHHHHH-H-------EEEEE-------- Seq: TTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPG SS: -EEEEEEE------EEEEEEE----------EE----------EEEEEEEEE--- Seq: EEQRYTCQVEHPGLDQPLIVIWEPSPSGTLVIGVISGIAVFVVILFIGILFIILR SS: ---EEEEEEEE------EEEEE---------HHHHHHHHHHHHHHHHHHHHHHHH Seq: KRQGSRGAMGHYVLAERE SS: HH----------------
Comparison with DSSP
Because, the PDB sequence is not complete, the dssp assignment is also incomplete. The interessting parts - the signal peptide and the cytoplasmic part - which are predicted as disordered are not covered by DSSP. PSIPRED and JPred predicted the transmembrane region well and also made no assignment to the - as disordered predicted - N- and C-terminus.
UniProt: ---------------------------EEEEEEEEEEE----EEE--EEEEEE--EEEEE DSSP: --EEEEEEEEEEB-SS-SSB--EEEEEETTEEEEE PSIPRED: CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEECCEEEEE JPred: ------HHHHHHHHHHHHH---------EEEEEEEEE-------EEEEEEEEE--EEEEE AA: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF DSSPSeq: RSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF 10 20 30 40 50 60 UniProt: EEEEE--EEE--------TTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-EEE--EEEE DSSP: EESSS--EEE-STTS-SSTTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SSS--EEEE PSIPRED: ECCCCCCEEECCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCEEEE JPred: E-----EEEE----------HHHHHHHHHHHHHHHHHHHHHHHHHH---------EEEEE AA: YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV DSSPSEQ: YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV 70 80 90 100 110 120 UniProt: EEEEEE-----EEEEEEEEE--EEEEEEEHHH-EEEEEE---HHHHHHHH---HHHHHHH DSSP: EEEEEE-TTS-EEEEEEEEETTEEEEEEEGGGTEEEESSGGGHHHHHHHHSSTHHHHHHH PSIPRED: EEEEEEECCCEEEEEEEEEECCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH JPred: EEEEE------EEEEEEE-----EEEEEE----EEE-------HHHHHHH--HHHHHHHH AA: ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR DSSPSEQ: ILGaEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR 130 140 150 160 170 180 UniProt: HHHH-HHHHHHHHHHHHHTTT-------EEEEEEEE----EEEEEEEEEEEEE--EEEEE DSSP: HHHHTHHHHHHHHHHHHHTTTSS--B--EEEEEEEE-SS-EEEEEEEEEEBSS--EEEEE PSIPRED: HHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCEEEEEEEEEECCCCEEEEEE JPred: HH------HHHHHHHHHH-H-------EEEEE---------EEEEEEE------EEEEEE AA: AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL DSSPSEQ: AYLERDaPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRbRALNYYPQNITMKWL 190 200 210 220 230 240 UniProt: E------HHH----EEEE-----EEEEEEEEE---HHHHEEEEEE---EEE-EEEE---- DSSP: ETTEE--GGGS---EEEE-TTS-EEEEEEEEE-TTGGGGEEEEEE-TTSSS-EEEE- PSIPRED: ECCEECCCCCCCCCCCEECCCCCEEEEEEEEECCCCCCCEEEEEECCCCCCCEEEEEECC JPred: E----------EE----------EEEEEEEEE------EEEEEEEE------EEEEE--- AA: KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS DSSPSEQ: KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTbQVEHPGLDQPLIVIW 250 260 270 280 290 300 UniProt: ------------------------------------------------ DSSP: PSIPRED: CCCCCEEEEEEEEEEEEEEEEEEEEEEEEEECCCCCCCCCCEEECCCC JPred: ------HHHHHHHHHHHHHHHHHHHHHHHHHH---------------- AA: PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE DSSPSEQ: 310 320 330 340
Prediction of disordered regions
DISOPRED
For the prediction, we used the DISOPRED-Server at http://bioinf.cs.ucl.ac.uk/disopred/
Disopred predictes two disordered residues at the signal peptide and a disordered region at the end of the sequence which is located inside the cell.
AA:Target sequence Pred:Residue disorder prediction(.)= ordered residue(*)=Disordered residue conf:997600000000000000000000000000000000000000000000000000000000 pred:**.......................................................... AA:MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF 10 20 30 40 50 60 conf:000120011000000000000000000000000000000000000000000000000000 pred:............................................................ AA:YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV 70 80 90 100 110 120 conf:000000000000000000000000000000000000000000000000000000000000 pred:............................................................ AA:ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR 130 140 150 160 170 180 conf:000000000000000000000002456777878777766530000000000000000000 pred:..............................*.*........................... AA:AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL 190 200 210 220 230 240 conf:000035555545543000000000000000000000000000000000000001354667 pred:............................................................ AA:KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS 250 260 270 280 290 300 conf:777766643300000000000000047889999999999999898999 pred:...........................********************* AA:PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE 310 320 330 340 DISOPRED predictions for a false positive rate threshold of: 2%
POODLE
POODLE stands for Prediction Of Order and Disorder by machine LEarning.
POODLE provides three different predictions
- POODLE-S: short disorder regions prediction
- POODLE-L: long disorder regions prediction (longer 40 residues)
- unfolded protein prediction
All POODLE variants predict a disordered region at the end of the protein which contains a transmembrane region (pos: 307-330), this shows an evidance for a disordered region at the C-Terminus. But also, all variants predict a short disordered region at the beginning of the sequence which is a part of the signal peptid (pos: 1-22).
POODLE-I
POODLE-I (series only) predicted 4 disordered regions within the protein sequence.
MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF **************---------------------------------------------- YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV -------**********---******------*--------------------------- ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR ------------------------------------------------------------ AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL ---------------------***************------------------------ KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS ----*********----------------------------------------******* PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE ************************************************
POODLE-S
POODLE-S (using missing residues) predicts 6 short disordered regions within the protein sequence.
MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF -**************--------------------------------------------- YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV -------**********---******---------------------------------- ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR ------------------------------------------------------------ AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL ---------------------***************------------------------ KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS ----*********----------------------------------------******* PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE *--------------------------------********-------
POODLE-S (using High B-Factor residues) predicts 2 short disordered regions within the protein sequence.
MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF -*-***------------------------------------------------------ YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV ------------------------------------------------------------ ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR ------------------------------------------------******------ AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL ------------------------------------------------------------ KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS ------------------------------------------------------------ PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE ------------------------------------------------
POODLE-L
POODLE-L predicts a disordered region from 296 to the end.
MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF ------------------------------------------------------------ YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV ------------------------------------------------------------ ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR ------------------------------------------------------------ AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL ------------------------------------------------------------ KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS ------------------------------------------------------****** PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE ************************************************
IUPRED
The short term prediction predicts 5 short regions. There are also disordered residues at the beginning and in the signal peptide.
MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF ***--------------------------------------------------------- YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV ------------------------------------------------------------ ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR ------------------------------------------------------------ AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL ------------------------------------------------------------ KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS ---------********----------***--------*-****---------------- PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE ---------------------------------------------***
The long term prediction predicted 7 disordered residues, but just one short region.
MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF ------------------------------------------------------------ YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV ------------------------------------------------------------ ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR ------------------------------------------------------------ AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL ------------------------------------------------------------ KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS ---------******-------------------------*------------------- PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE ------------------------------------------------
The prediction of sturcured regions predicts one globular domain from 1-348. This means, that the whole protein is structured. This is a contradiction to the prediction of POODLE, but because of the weak evidence given by the other IUPRED-methods not a real contradiction to the other results of IUPRED.
META-Disorder
For this task, we used the Server at https://www.predictprotein.org.
predicted secondary structure composision
sec str type | H | E | L |
---|---|---|---|
% in protein | 27.30 | 28.74 | 43.97 |
Prediction of disordered residiues
Number Residue NORSnet NORS2st PROFbval bval2st Ucon Ucon2st MD_raw MD_rel MD2st 1 M 0.18 - 0.99 D 0.37 - 0.515 0 - 2 G 0.12 - 0.80 D 0.33 - 0.485 1 - 3 P 0.05 - 0.69 D 0.20 - 0.414 3 - 4 R 0.07 - 0.65 D 0.15 - 0.374 4 - 5 A 0.05 - 0.33 - 0.14 - 0.323 6 - 6 R 0.05 - 0.30 - 0.13 - 0.283 7 - 7 P 0.11 - 0.26 - 0.13 - 0.270 8 - 8 A 0.12 - 0.23 - 0.14 - 0.253 8 - 9 L 0.10 - 0.18 - 0.18 - 0.253 8 - 10 L 0.11 - 0.16 - 0.16 - 0.263 8 - 11 L 0.09 - 0.15 - 0.16 - 0.273 8 - 12 L 0.08 - 0.15 - 0.17 - 0.283 7 - 13 M 0.07 - 0.16 - 0.20 - 0.293 7 - 14 L 0.06 - 0.17 - 0.20 - 0.270 8 - 15 L 0.06 - 0.20 - 0.15 - 0.273 8 - 16 Q 0.06 - 0.23 - 0.13 - 0.253 8 - 17 T 0.06 - 0.28 - 0.13 - 0.253 8 - 18 A 0.08 - 0.34 - 0.13 - 0.253 8 - 19 V 0.10 - 0.28 - 0.13 - 0.250 9 - 20 L 0.12 - 0.33 - 0.15 - 0.242 9 - 21 Q 0.11 - 0.30 - 0.14 - 0.242 9 - 22 G 0.13 - 0.42 - 0.14 - 0.242 9 - 23 R 0.15 - 0.39 - 0.15 - 0.242 9 - 24 L 0.15 - 0.41 - 0.14 - 0.242 9 - 25 L 0.12 - 0.41 - 0.16 - 0.242 9 - 26 R 0.12 - 0.42 - 0.13 - 0.242 9 - 27 S 0.12 - 0.43 - 0.13 - 0.242 9 - 28 H 0.12 - 0.33 - 0.14 - 0.232 9 - 29 S 0.09 - 0.39 - 0.13 - 0.232 9 - 30 L 0.13 - 0.29 - 0.13 - 0.240 9 - 31 H 0.14 - 0.27 - 0.13 - 0.240 9 - 32 Y 0.19 - 0.17 - 0.13 - 0.232 9 - 33 L 0.21 - 0.16 - 0.13 - 0.240 9 - 34 F 0.14 - 0.20 - 0.13 - 0.240 9 - 35 M 0.13 - 0.20 - 0.16 - 0.242 9 - 36 G 0.12 - 0.23 - 0.14 - 0.250 9 - 37 A 0.10 - 0.39 - 0.16 - 0.242 9 - 38 S 0.12 - 0.46 - 0.16 - 0.253 8 - 39 E 0.21 - 0.44 - 0.23 - 0.260 8 - 40 Q 0.22 - 0.56 D 0.21 - 0.263 8 - 41 D 0.24 - 0.55 D 0.16 - 0.263 8 - 42 L 0.18 - 0.58 D 0.19 - 0.253 8 - 43 G 0.15 - 0.57 D 0.18 - 0.263 8 - 44 L 0.13 - 0.51 D 0.13 - 0.242 9 - 45 S 0.12 - 0.42 - 0.13 - 0.242 9 - 46 L 0.13 - 0.47 D 0.13 - 0.240 9 - 47 F 0.16 - 0.39 - 0.13 - 0.240 9 - 48 E 0.14 - 0.28 - 0.13 - 0.232 9 - 49 A 0.10 - 0.23 - 0.15 - 0.242 9 - 50 L 0.09 - 0.21 - 0.15 - 0.242 9 - 51 G 0.11 - 0.24 - 0.15 - 0.253 8 - 52 Y 0.08 - 0.28 - 0.15 - 0.253 8 - 53 V 0.06 - 0.45 - 0.13 - 0.242 9 - 54 D 0.05 - 0.47 D 0.13 - 0.263 8 - 55 D 0.06 - 0.43 - 0.13 - 0.253 8 - 56 Q 0.07 - 0.49 D 0.13 - 0.250 9 - 57 L 0.06 - 0.43 - 0.14 - 0.242 9 - 58 F 0.11 - 0.29 - 0.17 - 0.242 9 - 59 V 0.15 - 0.28 - 0.16 - 0.242 9 - 60 F 0.19 - 0.30 - 0.15 - 0.242 9 - 61 Y 0.29 - 0.28 - 0.14 - 0.242 9 - 62 D 0.29 - 0.41 - 0.15 - 0.253 8 - 63 H 0.23 - 0.55 D 0.23 - 0.263 8 - 64 E 0.25 - 0.65 D 0.31 - 0.313 6 - 65 S 0.25 - 0.68 D 0.47 - 0.313 6 - 66 R 0.25 - 0.69 D 0.63 D 0.313 6 - 67 R 0.25 - 0.66 D 0.57 - 0.283 7 - 68 V 0.35 - 0.67 D 0.46 - 0.283 7 - 69 E 0.46 - 0.64 D 0.31 - 0.283 7 - 70 P 0.45 - 0.52 D 0.31 - 0.290 7 - 71 R 0.41 - 0.47 D 0.32 - 0.293 7 - 72 T 0.45 - 0.59 D 0.32 - 0.333 6 - 73 P 0.45 - 0.60 D 0.31 - 0.323 6 - 74 W 0.32 - 0.47 D 0.27 - 0.313 6 - 75 V 0.29 - 0.55 D 0.27 - 0.323 6 - 76 S 0.26 - 0.60 D 0.30 - 0.323 6 - 77 S 0.23 - 0.71 D 0.23 - 0.354 5 - 78 R 0.17 - 0.69 D 0.17 - 0.323 6 - 79 I 0.18 - 0.76 D 0.17 - 0.313 6 - 80 S 0.18 - 0.72 D 0.22 - 0.310 6 - 81 S 0.19 - 0.69 D 0.17 - 0.293 7 - 82 Q 0.24 - 0.68 D 0.17 - 0.283 7 - 83 M 0.27 - 0.59 D 0.18 - 0.273 8 - 84 W 0.22 - 0.54 D 0.24 - 0.263 8 - 85 L 0.18 - 0.57 D 0.18 - 0.260 8 - 86 Q 0.16 - 0.52 D 0.20 - 0.263 8 - 87 L 0.13 - 0.50 D 0.18 - 0.253 8 - 88 S 0.14 - 0.52 D 0.18 - 0.283 7 - 89 Q 0.14 - 0.59 D 0.27 - 0.293 7 - 90 S 0.16 - 0.56 D 0.33 - 0.303 7 - 91 L 0.17 - 0.56 D 0.24 - 0.303 7 - 92 K 0.14 - 0.55 D 0.23 - 0.293 7 - 93 G 0.13 - 0.55 D 0.22 - 0.283 7 - 94 W 0.11 - 0.52 D 0.17 - 0.283 7 - 95 D 0.10 - 0.54 D 0.19 - 0.283 7 - 96 H 0.09 - 0.54 D 0.19 - 0.280 7 - 97 M 0.11 - 0.47 D 0.14 - 0.283 7 - 98 F 0.12 - 0.44 - 0.14 - 0.283 7 - 99 T 0.09 - 0.45 - 0.14 - 0.283 7 - 100 V 0.10 - 0.47 D 0.13 - 0.283 7 - 101 D 0.12 - 0.41 - 0.14 - 0.273 8 - 102 F 0.11 - 0.40 - 0.15 - 0.293 7 - 103 W 0.10 - 0.51 D 0.18 - 0.293 7 - 104 T 0.13 - 0.46 - 0.18 - 0.293 7 - 105 I 0.19 - 0.39 - 0.20 - 0.293 7 - 106 M 0.17 - 0.47 D 0.18 - 0.303 7 - 107 E 0.21 - 0.51 D 0.32 - 0.323 6 - 108 N 0.18 - 0.47 D 0.52 - 0.360 5 - 109 H 0.15 - 0.52 D 0.55 - 0.354 5 - 110 N 0.15 - 0.56 D 0.63 D 0.323 6 - 111 H 0.15 - 0.62 D 0.76 D 0.333 6 - 112 S 0.16 - 0.66 D 0.54 - 0.313 6 - 113 K 0.17 - 0.67 D 0.57 - 0.303 7 - 114 E 0.15 - 0.53 D 0.55 - 0.303 7 - 115 S 0.12 - 0.49 D 0.42 - 0.273 8 - 116 H 0.14 - 0.34 - 0.36 - 0.263 8 - 117 T 0.11 - 0.34 - 0.33 - 0.260 8 - 118 L 0.10 - 0.26 - 0.20 - 0.253 8 - 119 Q 0.09 - 0.28 - 0.20 - 0.253 8 - 120 V 0.17 - 0.34 - 0.16 - 0.260 8 - 121 I 0.20 - 0.33 - 0.19 - 0.263 8 - 122 L 0.16 - 0.28 - 0.21 - 0.273 8 - 123 G 0.15 - 0.34 - 0.32 - 0.283 7 - 124 C 0.14 - 0.32 - 0.30 - 0.293 7 - 125 E 0.16 - 0.47 D 0.38 - 0.313 6 - 126 M 0.15 - 0.49 D 0.48 - 0.333 6 - 127 Q 0.14 - 0.66 D 0.69 D 0.343 5 - 128 E 0.14 - 0.73 D 0.69 D 0.343 5 - 129 D 0.16 - 0.69 D 0.67 D 0.343 5 - 130 N 0.16 - 0.66 D 0.44 - 0.323 6 - 131 S 0.13 - 0.66 D 0.69 D 0.310 6 - 132 T 0.13 - 0.59 D 0.49 - 0.283 7 - 133 E 0.16 - 0.54 D 0.40 - 0.273 8 - 134 G 0.25 - 0.42 - 0.25 - 0.280 7 - 135 Y 0.21 - 0.36 - 0.28 - 0.263 8 - 136 W 0.17 - 0.39 - 0.26 - 0.260 8 - 137 K 0.14 - 0.36 - 0.28 - 0.273 8 - 138 Y 0.12 - 0.35 - 0.27 - 0.283 7 - 139 G 0.10 - 0.41 - 0.26 - 0.283 7 - 140 Y 0.08 - 0.43 - 0.27 - 0.283 7 - 141 D 0.09 - 0.61 D 0.43 - 0.290 7 - 142 G 0.09 - 0.57 D 0.24 - 0.280 7 - 143 Q 0.09 - 0.47 D 0.25 - 0.283 7 - 144 D 0.09 - 0.53 D 0.28 - 0.280 7 - 145 H 0.11 - 0.41 - 0.44 - 0.273 8 - 146 L 0.12 - 0.35 - 0.38 - 0.263 8 - 147 E 0.14 - 0.38 - 0.30 - 0.263 8 - 148 F 0.12 - 0.39 - 0.32 - 0.260 8 - 149 C 0.13 - 0.48 D 0.20 - 0.280 7 - 150 P 0.11 - 0.67 D 0.23 - 0.293 7 - 151 D 0.15 - 0.65 D 0.29 - 0.343 5 - 152 T 0.18 - 0.64 D 0.24 - 0.364 5 - 153 L 0.15 - 0.57 D 0.39 - 0.343 5 - 154 D 0.11 - 0.55 D 0.55 - 0.340 5 - 155 W 0.18 - 0.41 - 0.53 - 0.313 6 - 156 R 0.20 - 0.41 - 0.45 - 0.300 7 - 157 A 0.16 - 0.41 - 0.33 - 0.313 6 - 158 A 0.18 - 0.49 D 0.48 - 0.333 6 - 159 E 0.16 - 0.55 D 0.41 - 0.404 3 - 160 P 0.14 - 0.56 D 0.70 D 0.424 3 - 161 R 0.11 - 0.56 D 0.55 - 0.414 3 - 162 A 0.14 - 0.51 D 0.65 D 0.374 4 - 163 W 0.15 - 0.55 D 0.50 - 0.354 5 - 164 P 0.24 - 0.57 D 0.50 - 0.354 5 - 165 T 0.25 - 0.56 D 0.48 - 0.330 6 - 166 K 0.23 - 0.61 D 0.43 - 0.343 5 - 167 L 0.15 - 0.60 D 0.57 - 0.333 6 - 168 E 0.13 - 0.59 D 0.59 D 0.333 6 - 169 W 0.14 - 0.58 D 0.56 - 0.330 6 - 170 E 0.10 - 0.69 D 0.55 - 0.333 6 - 171 R 0.10 - 0.69 D 0.43 - 0.333 6 - 172 H 0.10 - 0.62 D 0.60 D 0.354 5 - 173 K 0.10 - 0.67 D 0.54 - 0.354 5 - 174 I 0.09 - 0.60 D 0.70 D 0.354 5 - 175 R 0.09 - 0.53 D 0.61 D 0.310 6 - 176 A 0.11 - 0.52 D 0.45 - 0.293 7 - 177 R 0.11 - 0.53 D 0.36 - 0.293 7 - 178 Q 0.12 - 0.49 D 0.32 - 0.283 7 - 179 N 0.12 - 0.47 D 0.44 - 0.293 7 - 180 R 0.09 - 0.47 D 0.50 - 0.313 6 - 181 A 0.10 - 0.45 - 0.39 - 0.300 7 - 182 Y 0.10 - 0.45 - 0.41 - 0.293 7 - 183 L 0.09 - 0.40 - 0.37 - 0.283 7 - 184 E 0.06 - 0.49 D 0.40 - 0.303 7 - 185 R 0.07 - 0.48 D 0.29 - 0.313 6 - 186 D 0.07 - 0.46 - 0.33 - 0.313 6 - 187 C 0.07 - 0.39 - 0.49 - 0.313 6 - 188 P 0.08 - 0.45 - 0.49 - 0.323 6 - 189 A 0.10 - 0.51 D 0.31 - 0.333 6 - 190 Q 0.10 - 0.35 - 0.35 - 0.293 7 - 191 L 0.10 - 0.34 - 0.23 - 0.293 7 - 192 Q 0.10 - 0.53 D 0.29 - 0.333 6 - 193 Q 0.12 - 0.47 D 0.28 - 0.323 6 - 194 L 0.12 - 0.45 - 0.27 - 0.313 6 - 195 L 0.12 - 0.55 D 0.21 - 0.323 6 - 196 E 0.13 - 0.64 D 0.21 - 0.330 6 - 197 L 0.16 - 0.58 D 0.23 - 0.343 5 - 198 G 0.22 - 0.59 D 0.23 - 0.343 5 - 199 R 0.24 - 0.62 D 0.33 - 0.354 5 - 200 G 0.27 - 0.64 D 0.36 - 0.374 4 - 201 V 0.33 - 0.61 D 0.33 - 0.354 5 - 202 L 0.31 - 0.61 D 0.47 - 0.343 5 - 203 D 0.32 - 0.68 D 0.37 - 0.343 5 - 204 Q 0.41 - 0.69 D 0.29 - 0.384 4 - 205 Q 0.39 - 0.70 D 0.40 - 0.404 3 - 206 V 0.34 - 0.66 D 0.39 - 0.404 3 - 207 P 0.29 - 0.64 D 0.53 - 0.414 3 - 208 P 0.28 - 0.60 D 0.43 - 0.394 4 - 209 L 0.34 - 0.58 D 0.36 - 0.364 5 - 210 V 0.40 - 0.51 D 0.27 - 0.343 5 - 211 K 0.45 - 0.48 D 0.33 - 0.343 5 - 212 V 0.45 - 0.53 D 0.33 - 0.333 6 - 213 T 0.46 - 0.55 D 0.34 - 0.354 5 - 214 H 0.43 - 0.57 D 0.37 - 0.374 4 - 215 H 0.32 - 0.63 D 0.46 - 0.364 5 - 216 V 0.25 - 0.69 D 0.34 - 0.333 6 - 217 T 0.32 - 0.69 D 0.31 - 0.347 5 - 218 S 0.21 - 0.74 D 0.33 - 0.343 5 - 219 S 0.16 - 0.70 D 0.27 - 0.333 6 - 220 V 0.14 - 0.68 D 0.30 - 0.293 7 - 221 T 0.16 - 0.54 D 0.36 - 0.273 8 - 222 T 0.16 - 0.38 - 0.26 - 0.253 8 - 223 L 0.19 - 0.20 - 0.25 - 0.242 9 - 224 R 0.18 - 0.17 - 0.18 - 0.242 9 - 225 C 0.21 - 0.18 - 0.17 - 0.250 9 - 226 R 0.23 - 0.18 - 0.18 - 0.253 8 - 227 A 0.15 - 0.17 - 0.19 - 0.253 8 - 228 L 0.08 - 0.23 - 0.25 - 0.263 8 - 229 N 0.08 - 0.32 - 0.19 - 0.263 8 - 230 Y 0.09 - 0.35 - 0.24 - 0.263 8 - 231 Y 0.07 - 0.38 - 0.18 - 0.253 8 - 232 P 0.06 - 0.47 D 0.23 - 0.260 8 - 233 Q 0.05 - 0.57 D 0.23 - 0.260 8 - 234 N 0.05 - 0.56 D 0.17 - 0.260 8 - 235 I 0.08 - 0.41 - 0.28 - 0.263 8 - 236 T 0.10 - 0.39 - 0.45 - 0.280 7 - 237 M 0.10 - 0.28 - 0.55 - 0.273 8 - 238 K 0.12 - 0.29 - 0.55 - 0.283 7 - 239 W 0.18 - 0.31 - 0.56 - 0.293 7 - 240 L 0.16 - 0.46 - 0.56 - 0.330 6 - 241 K 0.09 - 0.56 D 0.65 D 0.364 5 - 242 D 0.13 - 0.70 D 0.76 D 0.444 2 - 243 K 0.13 - 0.69 D 0.76 D 0.480 1 - 244 Q 0.13 - 0.66 D 0.93 D 0.531 0 D 245 P 0.17 - 0.73 D 0.92 D 0.520 0 D 246 M 0.28 - 0.65 D 0.90 D 0.525 0 D 247 D 0.31 - 0.68 D 0.87 D 0.515 0 - 248 A 0.36 - 0.70 D 0.87 D 0.520 0 D 249 K 0.40 - 0.69 D 0.89 D 0.485 1 - 250 E 0.41 - 0.67 D 0.79 D 0.490 1 - 251 F 0.32 - 0.65 D 0.76 D 0.469 1 - 252 E 0.41 - 0.66 D 0.69 D 0.465 1 - 253 P 0.55 D 0.57 D 0.74 D 0.515 0 - 254 K 0.47 - 0.54 D 0.56 - 0.455 2 - 255 D 0.39 - 0.59 D 0.56 - 0.384 4 - 256 V 0.36 - 0.59 D 0.70 D 0.394 4 - 257 L 0.29 - 0.51 D 0.59 D 0.343 5 - 258 P 0.31 - 0.56 D 0.42 - 0.343 5 - 259 N 0.27 - 0.60 D 0.34 - 0.337 6 - 260 G 0.23 - 0.65 D 0.26 - 0.354 5 - 261 D 0.16 - 0.56 D 0.23 - 0.343 5 - 262 G 0.12 - 0.56 D 0.23 - 0.313 6 - 263 T 0.08 - 0.45 - 0.22 - 0.293 7 - 264 Y 0.08 - 0.41 - 0.16 - 0.273 8 - 265 Q 0.06 - 0.40 - 0.16 - 0.263 8 - 266 G 0.10 - 0.36 - 0.13 - 0.253 8 - 267 W 0.11 - 0.29 - 0.13 - 0.253 8 - 268 I 0.09 - 0.28 - 0.14 - 0.253 8 - 269 T 0.12 - 0.29 - 0.15 - 0.270 8 - 270 L 0.14 - 0.28 - 0.16 - 0.270 8 - 271 A 0.15 - 0.40 - 0.19 - 0.283 7 - 272 V 0.10 - 0.43 - 0.29 - 0.283 7 - 273 P 0.09 - 0.51 D 0.43 - 0.273 8 - 274 P 0.11 - 0.65 D 0.31 - 0.273 8 - 275 G 0.11 - 0.80 D 0.45 - 0.290 7 - 276 E 0.10 - 0.79 D 0.35 - 0.273 8 - 277 E 0.08 - 0.78 D 0.50 - 0.293 7 - 278 Q 0.07 - 0.69 D 0.36 - 0.273 8 - 279 R 0.10 - 0.57 D 0.42 - 0.273 8 - 280 Y 0.20 - 0.35 - 0.42 - 0.250 9 - 281 T 0.18 - 0.30 - 0.36 - 0.242 9 - 282 C 0.16 - 0.20 - 0.28 - 0.242 9 - 283 Q 0.21 - 0.26 - 0.19 - 0.250 9 - 284 V 0.24 - 0.28 - 0.21 - 0.253 8 - 285 E 0.16 - 0.36 - 0.31 - 0.263 8 - 286 H 0.13 - 0.36 - 0.33 - 0.283 7 - 287 P 0.15 - 0.61 D 0.32 - 0.293 7 - 288 G 0.16 - 0.56 D 0.22 - 0.293 7 - 289 L 0.19 - 0.62 D 0.22 - 0.280 7 - 290 D 0.16 - 0.70 D 0.15 - 0.280 7 - 291 Q 0.19 - 0.66 D 0.14 - 0.263 8 - 292 P 0.25 - 0.68 D 0.14 - 0.273 8 - 293 L 0.34 - 0.49 D 0.15 - 0.253 8 - 294 I 0.36 - 0.44 - 0.20 - 0.250 9 - 295 V 0.38 - 0.41 - 0.18 - 0.263 8 - 296 I 0.39 - 0.44 - 0.18 - 0.283 7 - 297 W 0.39 - 0.47 D 0.17 - 0.280 7 - 298 E 0.33 - 0.55 D 0.21 - 0.293 7 - 299 P 0.17 - 0.65 D 0.20 - 0.337 6 - 300 S 0.17 - 0.69 D 0.20 - 0.354 5 - 301 P 0.16 - 0.71 D 0.20 - 0.354 5 - 302 S 0.11 - 0.71 D 0.26 - 0.343 5 - 303 G 0.12 - 0.68 D 0.17 - 0.303 7 - 304 T 0.18 - 0.60 D 0.14 - 0.293 7 - 305 L 0.20 - 0.53 D 0.14 - 0.263 8 - 306 V 0.16 - 0.40 - 0.13 - 0.260 8 - 307 I 0.12 - 0.29 - 0.13 - 0.242 9 - 308 G 0.11 - 0.28 - 0.13 - 0.242 9 - 309 V 0.09 - 0.20 - 0.14 - 0.240 9 - 310 I 0.06 - 0.15 - 0.14 - 0.240 9 - 311 S 0.05 - 0.14 - 0.14 - 0.242 9 - 312 G 0.03 - 0.16 - 0.14 - 0.242 9 - 313 I 0.03 - 0.17 - 0.16 - 0.242 9 - 314 A 0.03 - 0.15 - 0.17 - 0.240 9 - 315 V 0.03 - 0.16 - 0.18 - 0.240 9 - 316 F 0.03 - 0.14 - 0.26 - 0.240 9 - 317 V 0.03 - 0.14 - 0.26 - 0.232 9 - 318 V 0.04 - 0.14 - 0.26 - 0.232 9 - 319 I 0.04 - 0.14 - 0.37 - 0.242 9 - 320 L 0.04 - 0.15 - 0.42 - 0.240 9 - 321 F 0.03 - 0.12 - 0.40 - 0.242 9 - 322 I 0.03 - 0.15 - 0.43 - 0.242 9 - 323 G 0.03 - 0.15 - 0.48 - 0.242 9 - 324 I 0.03 - 0.17 - 0.33 - 0.232 9 - 325 L 0.03 - 0.16 - 0.18 - 0.232 9 - 326 F 0.04 - 0.18 - 0.14 - 0.232 9 - 327 I 0.05 - 0.23 - 0.13 - 0.232 9 - 328 I 0.06 - 0.28 - 0.13 - 0.232 9 - 329 L 0.06 - 0.33 - 0.14 - 0.240 9 - 330 R 0.07 - 0.40 - 0.17 - 0.250 9 - 331 K 0.07 - 0.47 D 0.23 - 0.273 8 - 332 R 0.09 - 0.56 D 0.29 - 0.313 6 - 333 Q 0.16 - 0.64 D 0.29 - 0.364 5 - 334 G 0.23 - 0.70 D 0.40 - 0.434 2 - 335 S 0.25 - 0.76 D 0.35 - 0.414 3 - 336 R 0.36 - 0.76 D 0.20 - 0.404 3 - 337 G 0.43 - 0.77 D 0.15 - 0.414 3 - 338 A 0.47 - 0.73 D 0.13 - 0.408 3 - 339 M 0.57 D 0.69 D 0.13 - 0.414 3 - 340 G 0.59 D 0.56 D 0.13 - 0.404 3 - 341 H 0.62 D 0.56 D 0.13 - 0.414 3 - 342 Y 0.39 - 0.47 D 0.14 - 0.439 2 - 343 V 0.34 - 0.47 D 0.15 - 0.469 1 - 344 L 0.37 - 0.59 D 0.18 - 0.515 0 - 345 A 0.35 - 0.74 D 0.17 - 0.515 0 - 346 E 0.31 - 0.89 D 0.17 - 0.520 0 D 347 R 0.35 - 0.91 D 0.23 - 0.525 0 D 348 E 0.34 - 0.92 D 0.38 - 0.520 0 D
Key for output ---------------- Number - residue number Residue - amino-acid type NORSnet - raw score by NORSnet (prediction of unstructured loops) NORS2st - two-state prediction by NORSnet; D=disordered PROFbval - raw score by PROFbval (prediction of residue flexibility from sequence) Bval2st - two-state prediction by PROFbval Ucon - raw score by Ucon (prediction of protein disorder using predicted internal contacts) Ucon2st - two-state prediction by Ucon MD - raw score by MD (prediction of protein disorder using orthogonal sources) MD_rel - reliability of the prediction by MD; values range from 0-9. 9=strong prediction MD2st - two-state prediction by MD
Prediction of transmembrane alpha-helices and signal peptides
TMHMM
Phobius and PolyPhobius
For Phobius and PolyPhobius, we used http://phobius.sbc.su.se/ with standard settings.
Phobius
Phobius predicts very accurate as seen below. The transmembrane region is predicted just 1-2 residues upstream from the annotated region. The same holds for the topological domains before and after the transmembrane region. Also the signal peptid is correctly predicted.
PREDICTED ANNOTATION ID sp|Q30201|HFE_HUMAN FT SIGNAL 1 21 | 1-20 FT REGION 1 7 N-REGION. FT REGION 8 16 H-REGION. FT REGION 17 21 C-REGION. FT TOPO_DOM 22 304 NON CYTOPLASMIC. | 23-306 FT TRANSMEM 305 329 | 307-330 FT TOPO_DOM 330 348 CYTOPLASMIC. | 331-348
PolyPhobius
PolyPhobius also predicts very accurate but in our case not as accurate as Phobius.
PREDICTED ANNOTATION ID sp|Q30201|HFE_HUMAN FT SIGNAL 1 23 | 1-20 FT REGION 1 5 N-REGION. FT REGION 6 19 H-REGION. FT REGION 20 23 C-REGION. FT TOPO_DOM 24 304 NON CYTOPLASMIC. | 23-306 FT TRANSMEM 305 329 | 307-330 FT TOPO_DOM 330 348 CYTOPLASMIC. | 331-348
OCTOPUS and SPOCTOPUS
Both, OCTOPUS and SPOCTOPUS predict the signal peptide and the transmembrane region correctly.
SignalP
TargetP
TargetP does not predict the signal peptide of the HFE-protein.
### targetp v1.1 prediction results ################################## Number of query sequences: 1 Cleavage site predictions not included. Using NON-PLANT networks. Name Len mTP SP other Loc RC ---------------------------------------------------------------------- sp_Q30201_HFE_HUMAN 348 0.433 0.912 0.004 S 3 ---------------------------------------------------------------------- cutoff 0.000 0.000 0.000
Prediction of GO terms
general
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 overlap 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
ProtFun is an ab initio prediction server.
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
Reference
<references />