Sequence-based predictions

Secondary structure prediction

PSIPRED

Secondary Structure predicted by 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

DISOPRED prediction profile for the HFE protein

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.

Distribution of disordered region over the AS-Sequence predicted by POODLE-I

MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF
**************----------------------------------------------
YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV
-------**********---******------*---------------------------
ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR
------------------------------------------------------------
AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL
---------------------***************------------------------
KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS
----*********----------------------------------------*******
PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
************************************************

POODLE-S

POODLE-S (using missing residues) predicts 6 short disordered regions within the protein sequence.

Distribution of disordered region over the AS-Sequence predicted by POODLE-S(Missing residues)

MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF
-**************---------------------------------------------
YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV
-------**********---******----------------------------------
ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR
------------------------------------------------------------
AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL
---------------------***************------------------------
KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS
----*********----------------------------------------*******
PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
*--------------------------------********-------

POODLE-S (using High B-Factor residues) predicts 2 short disordered regions within the protein sequence.

Distribution of disordered region over the AS-Sequence predicted by POODLE-S(High B-Factor residues)

MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF
-*-***------------------------------------------------------
YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV
------------------------------------------------------------
ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR
------------------------------------------------******------
AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL
------------------------------------------------------------
KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS
------------------------------------------------------------
PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
------------------------------------------------

POODLE-L

POODLE-L predicts a disordered region from 296 to the end.

Distribution of disordered region over the AS-Sequence predicted by POODLE-L

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.

IUPRED prediction of short regions

MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF 
***---------------------------------------------------------
YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV 
------------------------------------------------------------
ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR 
------------------------------------------------------------
AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL 
------------------------------------------------------------
KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS 
---------********----------***--------*-****----------------
PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
---------------------------------------------***

The long term prediction predicted 7 disordered residues, but just one short region.

IUPRED prediction of long regions

MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF 
------------------------------------------------------------
YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV 
------------------------------------------------------------
ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR 
------------------------------------------------------------
AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL 
------------------------------------------------------------
KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS 
---------******-------------------------*-------------------
PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
------------------------------------------------

IUPRED prediction of structured regions

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

<A NAME="prof_body_pred">Prediction (brief)</A>  <a id="show_landscape" class="toggle">(Show Landscape View)</a> <a id="show_portrait" style="display: none;" class="toggle">(Show Portrait View)</a>

 
           ....,....1....,....2....,....3....,....4....,....5....,....6
<A HREF="#AA">AA </A>        MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF 
<A HREF="#OHEL">OBS_sec</A>                                                                
<A HREF="#PHEL">PROF_sec</A>       HHHHHHHHHHHHHHHHH        EEEEEEEE        EEEEEEEE   EEEE 
<A HREF="#RI_S">Rel_sec</A>    973114566667777521210010233203576754315666754156877522514676 
<A HREF="#SUBsec">SUB_sec</A>    LL....HHHHHHHHHH..............EEEEE...LLLLLL..EEEEEE..L..EEE 
 
<A HREF="#Obie">O_3_acc</A>    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb 
<A HREF="#Pbie">P_3_acc</A>    ee ebbbbbbbbbbbbbbbbb   b  bbbbbbbbbbb ee e  bbbbbbbbbbbbbbb 
<A HREF="#RI_A">Rel_acc</A>    520200358998765332221110210035146355212110221032547240111431 
<A HREF="#SUBacc">SUB_acc</A>    e......bbbbbbbb..............b.bb.bb............bbb.b....b..
 
 
           ....,....7....,....8....,....9....,....10...,....11...,....12
<A HREF="#AA">AA </A>        YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV 
<A HREF="#OHEL">OBS_sec</A>                                                                
<A HREF="#PHEL">PROF_sec</A>   E           HHHH     HHHHHHHHHHHHHHHHHHHHHHHHHHHH      EEEEE 
<A HREF="#RI_S">Rel_sec</A>    305544434531132102560013554332222224555556777754113566223556 
<A HREF="#SUBsec">SUB_sec</A>    ..LL.....L........LL....HH..........HHHHHHHHHHH....LLL...EEE 
 
<A HREF="#Obie">O_3_acc</A>    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb 
<A HREF="#Pbie">P_3_acc</A>    b be ee     ebbeeeeeee b ebbe beebe bb b bb bbe  e eee bbbbb 
<A HREF="#RI_A">Rel_acc</A>    300011201101101221011402211211141022121015023021211231111312 
<A HREF="#SUBacc">SUB_acc</A>    .....................e.........e.........b..................
 
 
           ....,....13...,....14...,....15...,....16...,....17...,....18
<A HREF="#AA">AA </A>        ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR 
<A HREF="#OHEL">OBS_sec</A>                                                                
<A HREF="#PHEL">PROF_sec</A>   EEEEEE       EEEEEE    EEEEE     EEEE      HHHHHHH HHHHHHHHH 
<A HREF="#RI_S">Rel_sec</A>    531232367530002354105311245404432132024100102444200024578877 
<A HREF="#SUBsec">SUB_sec</A>    E......LLL......E...L.....E...........................HHHHHH 
 
<A HREF="#Obie">O_3_acc</A>    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb 
<A HREF="#Pbie">P_3_acc</A>    bbbb b eeee e bb bbbebe bb bb ee eb bb eeb e eeebee eeebe b 
<A HREF="#RI_A">Rel_acc</A>    221521223210110011102012141301210301101000011022211111112102 
<A HREF="#SUBacc">SUB_acc</A>    ...b.....................b..................................
 
 
           ....,....19...,....20...,....21...,....22...,....23...,....24
<A HREF="#AA">AA </A>        AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL 
<A HREF="#OHEL">OBS_sec</A>                                                                
<A HREF="#PHEL">PROF_sec</A>   HHHHHHHHHHHHHHHHH            EEE         EEEEEEE      EEEEEE 
<A HREF="#RI_S">Rel_sec</A>    777655467787654203110245666500010234686504777642134551367875 
<A HREF="#SUBsec">SUB_sec</A>    HHHHHH.HHHHHHH.........LLLLL........LLLL..EEEE.....LL..EEEEE 
 
<A HREF="#Obie">O_3_acc</A>    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb 
<A HREF="#Pbie">P_3_acc</A>    ebb e b ebbeeb e bee beeeeee  eb   eeee b bbbbbbbbbb eb b bb 
<A HREF="#RI_A">Rel_acc</A>    203232623063231420210131211111201100121012809171230111636350 
<A HREF="#SUBacc">SUB_acc</A>    ......b...b....e..........................b.b.b.......b.b.b.
 
 
           ....,....25...,....26...,....27...,....28...,....29...,....30
<A HREF="#AA">AA </A>        KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS
<A HREF="#OHEL">OBS_sec</A>                                                                
<A HREF="#PHEL">PROF_sec</A>   E                      EEEEEEEEE      EEEEEEEE      EEEEE   
<A HREF="#RI_S">Rel_sec</A>    245302444322331012666312368887860676742678874135666514451246 
<A HREF="#SUBsec">SUB_sec</A>    ..L...............LLL....EEEEEEE.LLLL..EEEEE...LLLLL...E...L 
 
<A HREF="#Obie">O_3_acc</A>    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb 
<A HREF="#Pbie">P_3_acc</A>     eeee eeee e ee beeee bbb bb b b  eee  bbb b bee e ebbb b ee 
<A HREF="#RI_A">Rel_acc</A>    221221203312100110211002010325232023213108383001031101020101 
<A HREF="#SUBacc">SUB_acc</A>    .............................b...........b.b................
 
 
           ....,....31...,....32...,....33...,....34...,...
<A HREF="#AA">AA </A>        PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE 
<A HREF="#OHEL">OBS_sec</A>                                                    
<A HREF="#PHEL">PROF_sec</A>        EEEEEEHHHHHHHHHHHHHEEEEEEEE                
<A HREF="#RI_S">Rel_sec</A>    777522333201334455455432023454202346645544556678 
<A HREF="#SUBsec">SUB_sec</A>    LLLL............HH.HH.......E......LL.LL..LLLLLL 
 
<A HREF="#Obie">O_3_acc</A>    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb 
<A HREF="#Pbie">P_3_acc</A>    eee bbbbbbbbbbbbbbbbbbbbbbbbb   eeeeeee e    eee 
<A HREF="#RI_A">Rel_acc</A>    121010326654777899899766653421221022000111000347 
<A HREF="#SUBacc">SUB_acc</A>    ........bbbbbbbbbbbbbbbbbb.b..................ee 
 
 
 
           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10...,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20...,....21...,....22...,....23...,....24...,....25...,....26...,....27...,....28...,....29...,....30...,....31...,....32...,....33...,....34...,...
<A HREF="#AA">AA </A>        MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPSPSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE 
<A HREF="#OHEL">OBS_sec</A>                                                                                                                                                                                                                                                                                                                                                                
<A HREF="#PHEL">PROF_sec</A>       HHHHHHHHHHHHHHHHH        EEEEEEEE        EEEEEEEE   EEEEE           HHHH     HHHHHHHHHHHHHHHHHHHHHHHHHHHH      EEEEEEEEEEE       EEEEEE    EEEEE     EEEE      HHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHH            EEE         EEEEEEE      EEEEEEE                      EEEEEEEEE      EEEEEEEE      EEEEE        EEEEEEHHHHHHHHHHHHHEEEEEEEE                
<A HREF="#RI_S">Rel_sec</A>    973114566667777521210010233203576754315666754156877522514676305544434531132102560013554332222224555556777754113566223556531232367530002354105311245404432132024100102444200024578877777655467787654203110245666500010234686504777642134551367875245302444322331012666312368887860676742678874135666514451246777522333201334455455432023454202346645544556678 
<A HREF="#SUBsec">SUB_sec</A>    LL....HHHHHHHHHH..............EEEEE...LLLLLL..EEEEEE..L..EEE..LL.....L........LL....HH..........HHHHHHHHHHH....LLL...EEEE......LLL......E...L.....E...........................HHHHHHHHHHHH.HHHHHHH.........LLLLL........LLLL..EEEE.....LL..EEEEE..L...............LLL....EEEEEEE.LLLL..EEEEE...LLLLL...E...LLLLL............HH.HH.......E......LL.LL..LLLLLL 
 
<A HREF="#Obie">O_3_acc</A>    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb 
<A HREF="#Pbie">P_3_acc</A>    ee ebbbbbbbbbbbbbbbbb   b  bbbbbbbbbbb ee e  bbbbbbbbbbbbbbbb be ee     ebbeeeeeee b ebbe beebe bb b bb bbe  e eee bbbbbbbbb b eeee e bb bbbebe bb bb ee eb bb eeb e eeebee eeebe b ebb e b ebbeeb e bee beeeeee  eb   eeee b bbbbbbbbbb eb b bb eeee eeee e ee beeee bbb bb b b  eee  bbb b bee e ebbb b eeeee bbbbbbbbbbbbbbbbbbbbbbbbb   eeeeeee e    eee 
<A HREF="#RI_A">Rel_acc</A>    520200358998765332221110210035146355212110221032547240111431300011201101101221011402211211141022121015023021211231111312221521223210110011102012141301210301101000011022211111112102203232623063231420210131211111201100121012809171230111636350221221203312100110211002010325232023213108383001031101020101121010326654777899899766653421221022000111000347 
<A HREF="#SUBacc">SUB_acc</A>    e......bbbbbbbb..............b.bb.bb............bbb.b....b.......................e.........e.........b.....................b.....................b........................................b...b....e..........................b.b.b.......b.b.b..............................b...........b.b........................bbbbbbbbbbbbbbbbbb.b..................ee

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
  
predicted regions by 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
  
predicted regions by 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.


  
predicted regions by OCTOPUS

  
predicted regions by SPOCTOPUS


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 />