Difference between revisions of "ASPA Sequence Based Predictions"

From Bioinformatikpedia
(Meta-Disorder)
(Prediction of transmembrane alpha-helices and signal peptides)
Line 1,017: Line 1,017:
   
 
==Prediction of transmembrane alpha-helices and signal peptides==
 
==Prediction of transmembrane alpha-helices and signal peptides==
  +
  +
The results of this task are unequivocal: Aspartoacyclase does not contain any transmembrane regions. From a biological point of view this was to be expected, as Aspartoacyclase is known to be located in the cytosol.
   
 
===TMHMM===
 
===TMHMM===
 
Since the VM version could not be made to work, we used the server at http://www.cbs.dtu.dk/services/TMHMM/.
 
Since the VM version could not be made to work, we used the server at http://www.cbs.dtu.dk/services/TMHMM/.
  +
  +
TMHMM uses a hidden markov model to predict transmembrane helices in proteins. It was published in 1998 by E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.
  +
  +
Reference: [http://people.binf.ku.dk/~krogh/publications/ps/SonnhammerEtal98.pdf Original paper]
  +
  +
The hidden markov model used by TMHMM models the biological structure with states for helix turns, helix caps and loops on either side of the membrane, which are specially designed to model membrane insertion, too. The HMM probabilities were estimated both by using a maximum likelihood method and a discriminative method.
  +
  +
Results for Aspartoacyclase very clearly show absence of any sort of transmembrane structure, which is biologically sound.
   
 
[[File:Sp P45381 ACY2 HUMAN.gif]]
 
[[File:Sp P45381 ACY2 HUMAN.gif]]

Revision as of 03:18, 7 June 2011

Prediction of Secondary Structure Elements

PsiPred

PsiPred results for Aspartoacyclase
# PSIPRED HFORMAT (PSIPRED V3.0)

Conf: 987522213466199993246776008999999984450000587389976339987971
Pred: CCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEECCHHHHHH
  AA: MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
              10        20        30        40        50        60


Conf: 998788998878786647999999984999999999988199999997428994187898
Pred: CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCC
  AA: CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
              70        80        90       100       110       120


Conf: 999505864599448999999998762999737862048886301220027861499667
Pred: CCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHCCCCCCEEEEEC
  AA: NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
             130       140       150       160       170       180


Conf: 877898808999999999999998976406998899973479998113515579877700
Pred: CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEEEECCCCCCCCCE
  AA: PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
             190       200       210       220       230       240


Conf: 552467669998546888832213699778518622057770372000011102000100
Pred: EEECCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEECCCCHHCCCCHHHEECCE
  AA: AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
             250       260       270       280       290       300


Conf: 3544256113309
Pred: EEEEECCCEEECC
  AA: LTLNAKSIRCCLH
             310 

JPred3

JPred3 was published in 1998 by Christian Cole, Jonathan D. Barber and Geoffrey J. Barton.

Reference: Original paper, current version

JPred3 uses the JNet 2.0 algorithm to make its predictions. This algorithm generates profiles using PSI-Blast (which is used to build a position-specific scoring matrix) and HMMer (which is used to construct HMM profiles.) Both position-specific scoring matrix and the HMMs are used to predict secondary structure and solvent accessibility.

Input: A protein sequence or a pre-made MSA; a PDB database is needed, too, but provided by the JPred3 server.

MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYID
------------EEEEEEEE------HHHHHHHHHH---------EEEEEEEE-HHHHHH-----H



CDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSR
---------------------HHHHHHHHHHHHHH-------EEEEEE-----------EEEE---



NNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKM
-HHHHHHHHHHHH------EEEEEE---------HHEE----EEEEE---------HHHHHHHHHH



IKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLT
HHHHHHHHHHH----------EEEEEEEEEE----------EEEE----------------HHE--



LDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRCCLH
----EEEE----EEEEEEE-----HHH-HHHHHHHHEEE-----EEEE-

DSSP

DSSP (Define Secondary Structure of Proteins) is a software for secondary structure assignment and was published in 1983 by Wolfgang Kabsch and Chris Sander. Reference: Original paper

DSSP does not predict secondary structure from amino acid sequences; instead, it uses a 3D structure (a PDB file) to deduce the secondary structure from the 3D structure. To this end, DSSP examines the phi and psi angles and the C alpha positions in the protein backbone and H-bonds present in the structure; these are used to define "n-turns", which are H-bonds between the NH and CO groups of amino acids with sequence separations of 3-5 residues, and "bridges" with greater sequence separations. Repeating 4-turns are used to identify helices, repeating bridges identify beta sheets.

Input: A 3D structure (a PDB file, ID 2o53 in our case)

Output: (from [1])

    H = alpha helix
    B = residue in isolated beta-bridge
    E = extended strand, participates in beta ladder
    G = 3-helix (3/10 helix)
    I = 5 helix (pi helix)
    T = hydrogen bonded turn
    S = bend 

The results differ from those of the two secondary structure predictors, as the PDB file contains a dimer, whereas the Uniprot sequence only contains one domain (which is a sensible thing, since both domains are essentially identical.)

The prediction shows slight differences between both domains; we assume that reasons for this are slight differences in the actual 3D structure of the two chains as well as H-bonds between the two chains.

                     10        20        30        40        50        60
                      |         |         |         |         |         |
    1 -   60 EHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCD
    1 -   60     SSSSSS TTTT HHHHHHHHHHTT  333  TT SSSSSST HHHHHTTTT TTT
    1 -   60
    1 -   60 AA AA               A  AA AAA AA AAAA A A     AA  AAAA AAAA
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 LNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLIL
   61 -  120 333  THHHHTT   TTT HHHHHHHHHHHHH  TTTTTT TSSSSSSS TTT SSSSSS
   61 -  120       **  * * **            **   * *
   61 -  120   A  AAA  AAAAAAAAA   A   A  AA  AAA AA             A
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 EDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLR
  121 -  180 T TT HHHHHHHHHHHHHHTTT SSSSS   TT     3333TTSSSSSSSST  TT
  121 -  180              *  ** **
  121 -  180  A A A      AA AAA AAAA A    AAAAAA        AA       A  A   A
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 ADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQ
  181 -  240 HHHHHHHHHHHHHHHHHHHHHHTT     SSSSSSSSSSSS     TTT   TSS TTTT
  181 -  240
  181 -  240  A  AA AA  AA     AA  AAAA AA A A  A AAA A AAAAA A      AA
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 DQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSI
  241 -  300 T TTT   TTTSSSS TT  SSS  TTT  SSSTTT 333TTTT TSSSSSSSSSSS
  241 -  300
  241 -  300 AA  AA AAAAA  A  AAAAAA AAAAA A          AAA    A  AAA A A


  301 -  302 RC
  301 -  302
  301 -  302
  301 -  302 AA
 
                  310       320       330       340       350       360
                    |         |         |         |         |         |
  303 -  362 EHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCD
  303 -  362     SSSSSS TTTT HHHHHHHHHHHH 3333  TT SSSSSST HHHHHTT T TTT
  303 -  362
  303 -  362 AA AA                  AA AAA AA AAAA A A A   AA  AAAA AAAA
                  370       380       390       400       410       420
                    |         |         |         |         |         |
  363 -  422 LNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLIL
  363 -  422 333  THHHHTT   TTT HHHHHHHHHHHHH  TTTTTT TSSSSSSS TTT SSSSSS
  363 -  422       **  ***  *            **    ****
  363 -  422   A  AAA  AAAAAAAAA   A   A  AA  AAA AA             A
                  430       440       450       460       470       480
                    |         |         |         |         |         |
  423 -  482 EDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLR
  423 -  482 T TT HHHHHHHHHHHHHHTTT SSSSS  TTTT    3333TTSSSSSSSS   TT
  423 -  482
  423 -  482  A A A      AA AA  AAAA A    AAAAAA        AA       A      A
                  490       500       510       520       530       540
                    |         |         |         |         |         |
  483 -  542 ADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQ
  483 -  542 HHHHHHHHHHHHHHHHHHHHHHTT     SSSSSSSSSSSS     TTT   TSS TTTT
  483 -  542                             *** *
  483 -  542  A  AA AA  A      AA  A AA AA A A  A AAA A AAAAA A A    AA
                  550       560       570       580       590       600
                    |         |         |         |         |         |
  543 -  602 DQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSI
  543 -  602 T TTT   TTTSSSS TT  SSS  TTT  SSSTTT THHHHTT TSSSSSSSSSSS
  543 -  602                                                        *
  543 -  602 AA  AA AAAAA  A  AAAAAA AAAAA A          AAA    A AAAA A AA


  603 -  604 RC
  603 -  604
  603 -  604
  603 -  604 AA

Clearly solvent accessible: A; involved in symmetry contacts: *

All in all, the two prediction methods Psipred and JPred3 did a good job; they managed to predict most of the main secondary structure elements, with only minor variations in length and position of the individual helices/sheets and very minor variations between each other. A somewhat more detailed result from DSSP is to be expected, as it has pointedly better information to and merely assigns instead of actually predicting the secondary structure.

Prediction of disordered regions

DISOPRED

DISOPRED predicts native disorder in proteins. It was published in 2004 by Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF and Jones DT. Reference: [2]

DISOPRED uses linear support vector machines to predict disorder in a given protein sequence. A set of 750 proteins with high-quality structures was used as training data; to this end, PSI-Blast profiles were generated by aligning the training structures against a filtered database of protein structures. The resulting profiles were used to train the SVMs.

DISOPRED result graph for Aspartoacyclase
DISOPRED predictions for a false positive rate threshold of: 2%

conf: 999999999877640000000000000000000000000000000000000000000000
pred: **********..................................................
  AA: MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
              10        20        30        40        50        60

conf: 000000000000000356777788777654200000000000000000000000000000
pred: ......................**....................................
  AA: CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
              70        80        90       100       110       120

conf: 000000000000000000000000000000000000000000000000000000000000
pred: ............................................................
  AA: NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
             130       140       150       160       170       180

conf: 000000000000000000000000000000000000000000000000000000000000
pred: ............................................................
  AA: PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
             190       200       210       220       230       240

conf: 000000000000000000000000000000000000000000000000000000000000
pred: ............................................................
  AA: AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
             250       260       270       280       290       300

conf: 0000000000002
pred: .............
  AA: LTLNAKSIRCCLH
             310

Asterisks (*) represent disorder predictions and dots (.) 
prediction of order. The confidence estimates give a rough
indication of the probability that each residue is disordered.

POODLE

POODLE (Prediction Of Order and Disorder by machine LEarning) is a series of programs published between 2005 and 2008. We used the latest variant, POODLE-I, which was published in 2008 by S.Hirose, K.Shimizu, N.Inoue, S.Kanai and T.Noguchi.

Reference: S.Hirose, K.Shimizu, N.Inoue, S.Kanai and T.Noguchi, "Disordered region prediction by integrating POODLE series", CASP8 Proceedings 2008, 14-15.

Input: Protein amino acid sequence

POODLE-I is an integrated variant of other flavors of POODLE (-S and -L for short/long regions of disorder and -W for proteins that are mostly disordered) and several other tools like Psipred, JNet etc. It employs a rather involved workflow.

Custom-formatted output for Aspartoacyclase:

Aspa disopred.png


POS 1    M      T      S      C      H      I      A      E      E      H      I      
         -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
         0.461  0.444  0.413  0.401  0.418  0.461  0.537  0.644  0.693  0.62   0.468  


POS 12    Q      K      V      A      I      F      G      G      T      H      G      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.321  0.238  0.177  0.146  0.128  0.116  0.106  0.104  0.111  0.126  0.132  


POS 23    N      E      L      T      G      V      F      L      V      K      H      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.131  0.118  0.098  0.073  0.053  0.041  0.036  0.035  0.035  0.036  0.036  


POS 34    W      L      E      N      G      A      E      I      Q      R      T      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.038  0.045  0.06   0.081  0.099  0.119  0.133  0.146  0.147  0.143  0.129  


POS 45    G      L      E      V      K      P      F      I      T      N      P      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.111  0.09   0.073  0.062  0.054  0.047  0.039  0.033  0.033  0.037  0.041  


POS 56    R      A      V      K      K      C      T      R      Y      I      D      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.043  0.047  0.054  0.062  0.068  0.071  0.073  0.07   0.067  0.069  0.075  


POS 67    C      D      L      N      R      I      F      D      L      E      N      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.08   0.081  0.078  0.075  0.073  0.072  0.076  0.094  0.127  0.176  0.249  


POS 78    L      G      K      K      M      S      E      D      L      P      Y      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.403  0.554  0.737  0.766  0.804  0.755  0.682  0.65   0.632  0.636  0.583  


POS 89    E      V      R      R      A      Q      E      I      N      H      L      
          -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
          0.505  0.448  0.348  0.262  0.201  0.16   0.131  0.11   0.103  0.104  0.111  


POS 100    F      G      P      K      D      S      E      D      S      Y      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.116  0.117  0.108  0.089  0.067  0.049  0.039  0.034  0.033  0.035  


POS 110    D      I      I      F      D      L      H      N      T      T      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.038  0.041  0.043  0.043  0.042  0.041  0.042  0.045  0.052  0.06   


POS 120    S      N      M      G      C      T      L      I      L      E      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.07   0.081  0.092  0.101  0.109  0.111  0.107  0.096  0.085  0.072  


POS 130    D      S      R      N      N      F      L      I      Q      M      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.06   0.051  0.046  0.04   0.036  0.033  0.032  0.031  0.031  0.031  


POS 140    F      H      Y      I      K      T      S      L      A      P      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.033  0.036  0.04   0.043  0.046  0.049  0.05   0.053  0.055  0.059  


POS 150    L      P      C      Y      V      Y      L      I      E      H      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.065  0.073  0.088  0.103  0.115  0.119  0.118  0.111  0.104  0.104  


POS 160    P      S      L      K      Y      A      T      T      R      S      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.121  0.147  0.19   0.229  0.264  0.263  0.245  0.196  0.149  0.098  


POS 170    I      A      K      Y      P      V      G      I      E      V      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.069  0.053  0.051  0.057  0.066  0.08   0.093  0.102  0.103  0.099  


POS 180    G      P      Q      P      Q      G      V      L      R      A      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.096  0.094  0.095  0.095  0.099  0.098  0.099  0.095  0.094  0.086  


POS 190    D      I      L      D      Q      M      R      K      M      I      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.074  0.059  0.048  0.04   0.038  0.038  0.038  0.039  0.04   0.043  


POS 200    K      H      A      L      D      F      I      H      H      F      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.046  0.049  0.051  0.052  0.056  0.064  0.077  0.092  0.112  0.142  


POS 210    N      E      G      K      E      F      P      P      C      A      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.17   0.198  0.21   0.311  0.281  0.248  0.105  0.084  0.072  0.071  


POS 220    I      E      V      Y      K      I      I      E      K      V      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.069  0.065  0.06   0.056  0.052  0.054  0.062  0.076  0.105  0.141  


POS 230    D      Y      P      R      D      E      N      G      E      I      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.176  0.203  0.224  0.227  0.217  0.209  0.228  0.248  0.271  0.282  


POS 240    A      A      I      I      H      P      N      L      Q      D      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.289  0.269  0.24   0.208  0.188  0.169  0.155  0.152  0.167  0.193  


POS 250    Q      D      W      K      P      L      H      P      G      D      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.222  0.236  0.235  0.21   0.175  0.136  0.11   0.097  0.099  0.104  


POS 260    P      M      F      L      T      L      D      G      K      T      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.107  0.108  0.104  0.095  0.084  0.077  0.073  0.082  0.102  0.125  


POS 270    I      P      L      G      G      D      C      T      V      Y      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.144  0.162  0.169  0.166  0.156  0.149  0.133  0.117  0.099  0.089  


POS 280    P      V      F      V      N      E      A      A      Y      Y      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.077  0.072  0.067  0.064  0.066  0.082  0.122  0.184  0.241  0.279  


POS 290    E      K      K      E      A      F      A      K      T      T      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.282  0.264  0.236  0.229  0.238  0.257  0.263  0.252  0.231  0.222  


POS 300    K      L      T      L      N      A      K      S      I      R      
           -1     -1     -1     -1     -1     -1     -1     -1     -1     -1     
           0.246  0.278  0.305  0.31   0.303  0.277  0.263  0.371  0.382  0.38   


POS 310    C      C      L      H      
           -1     -1     -1     -1     
           0.348  0.51   0.496  0.489  

IUPRED

IUPRED is a software for the prediction of intrinsically unstructured regions in proteins. It was published in 2005 by Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon.

Reference: IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon, Bioinformatics (2005) 21, 3433-3434.

IUPRED predicts disordered regions by estimating the capacity of the amino acid chain to form stabilizing contacts. The underlying assumption is that proteins intrinsically unable to do so have distinct sequences that can be identified via their unfavorable energy values. To this end a 20x20 predictor matrix was calculated from a set of globular proteins with known structure. IUPRED uses this matrix to derive a tendency to be intrinsically unstructured from the amino acid composition alone.

Input: An amino acid sequence.

IUPRED comes in three flavors: Long Disorder, which specializes in finding long stretches of disorder, Short Disorder, which does the same for short stretches of disorder, and structured regions, which predicts regions lacking disorder.

Long Disorder

Aspa iupred1.png

POS 1    M      T      S      C      H      I      A      E      E      H      I      
         0.3215  0.3426  0.2817  0.2783  0.2064  0.1275  0.1554  0.1823  0.2094  0.2364  0.2575  


POS 12    Q      K      V      A      I      F      G      G      T      H      G      
          0.2988  0.3087  0.2364  0.3215  0.3149  0.3321  0.2609  0.1823  0.1275  0.1206  0.1759  


POS 23    N      E      L      T      G      V      F      L      V      K      H      
          0.1028  0.0676  0.1070  0.1298  0.1881  0.2575  0.2715  0.1969  0.2034  0.2034  0.2064  


POS 34    W      L      E      N      G      A      E      I      Q      R      T      
          0.1942  0.1206  0.1914  0.1399  0.1373  0.2064  0.2002  0.1969  0.2541  0.2715  0.2951  


POS 45    G      L      E      V      K      P      F      I      T      N      P      
          0.3840  0.4256  0.3460  0.3321  0.3286  0.2609  0.2503  0.3249  0.2292  0.1583  0.1611  


POS 56    R      A      V      K      K      C      T      R      Y      I      D      
          0.0985  0.1554  0.0929  0.1373  0.1424  0.0765  0.0749  0.1229  0.0749  0.0780  0.0719  


POS 67    C      D      L      N      R      I      F      D      L      E      N      
          0.0424  0.0506  0.0734  0.0734  0.0605  0.1048  0.1115  0.1184  0.1229  0.2064  0.1323  


POS 78    L      G      K      K      M      S      E      D      L      P      Y      
          0.2258  0.1643  0.2364  0.2292  0.2002  0.2884  0.4087  0.3215  0.4119  0.3948  0.3053  


POS 89    E      V      R      R      A      Q      E      I      N      H      L      
          0.2849  0.2849  0.3149  0.3182  0.3631  0.3667  0.3667  0.3631  0.4441  0.3286  0.4220  


POS 100    F      G      P      K      D      S      E      D      S      Y      
           0.3215  0.3053  0.1969  0.2034  0.1611  0.1501  0.1476  0.2224  0.2164  0.2164  


POS 110    D      I      I      F      D      L      H      N      T      T      
           0.3053  0.3704  0.3704  0.2609  0.2680  0.1823  0.1184  0.0662  0.0690  0.0734  


POS 120    S      N      M      G      C      T      L      I      L      E      
           0.1229  0.1184  0.1914  0.2817  0.2849  0.2034  0.2064  0.2193  0.1759  0.0985  


POS 130    D      S      R      N      N      F      L      I      Q      M      
           0.0948  0.0581  0.0327  0.0398  0.0414  0.0719  0.0414  0.0581  0.1092  0.1092  


POS 140    F      H      Y      I      K      T      S      L      A      P      
           0.1162  0.0662  0.0398  0.0269  0.0163  0.0105  0.0115  0.0184  0.0275  0.0300  


POS 150    L      P      C      Y      V      Y      L      I      E      H      
           0.0372  0.0433  0.0424  0.0405  0.0581  0.0618  0.0618  0.0618  0.1007  0.0749  


POS 160    P      S      L      K      Y      A      T      T      R      S      
           0.0543  0.0870  0.0443  0.0888  0.1007  0.1424  0.1449  0.2292  0.2470  0.2328  


POS 170    I      A      K      Y      P      V      G      I      E      V      
           0.2575  0.2503  0.2752  0.3667  0.3704  0.3948  0.3426  0.3356  0.3019  0.3149  


POS 180    G      P      Q      P      Q      G      V      L      R      A      
           0.2328  0.2328  0.2752  0.2951  0.3321  0.3087  0.3631  0.3182  0.3182  0.2918  


POS 190    D      I      L      D      Q      M      R      K      M      I      
           0.3494  0.3182  0.2164  0.2129  0.1115  0.0605  0.0592  0.0870  0.0734  0.0780  


POS 200    K      H      A      L      D      F      I      H      H      F      
           0.1048  0.0967  0.1501  0.2364  0.1349  0.1399  0.1942  0.1206  0.1048  0.0817  


POS 210    N      E      G      K      E      F      P      P      C      A      
           0.1449  0.1048  0.0618  0.0734  0.0704  0.0389  0.0835  0.1349  0.0948  0.1028  


POS 220    I      E      V      Y      K      I      I      E      K      V      
           0.1115  0.1184  0.1092  0.1184  0.1323  0.1275  0.2129  0.2094  0.1229  0.1731  


POS 230    D      Y      P      R      D      E      N      G      E      I      
           0.1731  0.1759  0.1028  0.1476  0.2470  0.2609  0.2680  0.3631  0.3566  0.3740  


POS 240    A      A      I      I      H      P      N      L      Q      D      
           0.4476  0.3392  0.4256  0.4256  0.3460  0.3356  0.3392  0.3249  0.3392  0.3460  


POS 250    Q      D      W      K      P      L      H      P      G      D      
           0.3910  0.3215  0.2783  0.3631  0.3667  0.3774  0.3566  0.3392  0.4220  0.3321  


POS 260    P      M      F      L      T      L      D      G      K      T      
           0.3426  0.2541  0.2436  0.3426  0.3566  0.2470  0.3286  0.2680  0.1643  0.1852  


POS 270    I      P      L      G      G      D      C      T      V      Y      
           0.1298  0.0631  0.0543  0.1048  0.1731  0.1449  0.1881  0.1115  0.0646  0.0734  


POS 280    P      V      F      V      N      E      A      A      Y      Y      
           0.0690  0.1092  0.1048  0.1399  0.0765  0.0646  0.0581  0.1028  0.1007  0.1373  


POS 290    E      K      K      E      A      F      A      K      T      T      
           0.1449  0.1298  0.1184  0.2034  0.2364  0.2164  0.2002  0.1583  0.1823  0.1852  


POS 300    K      L      T      L      N      A      K      S      I      R      
           0.1881  0.1184  0.1184  0.1184  0.0888  0.0851  0.1349  0.1349  0.1137  0.0870 


POS 310    C      C      L      H      
           0.0631  0.0473  0.0734  0.0483  

Short Disorder

Aspa iupred2.png

POS 1    M      T      S      C      H      I      A      E      E      H      I      
         0.8886  0.7772  0.7418  0.6984  0.5992  0.5296  0.4149  0.2748  0.2333  0.1921  0.1566  


POS 12    Q      K      V      A      I      F      G      G      T      H      G      
          0.1805  0.1844  0.1732  0.2700  0.1766  0.2531  0.2913  0.2080  0.1292  0.0832  0.0965  


POS 23    N      E      L      T      G      V      F      L      V      K      H      
          0.0909  0.0991  0.0935  0.0660  0.1088  0.1766  0.1766  0.1495  0.1566  0.0991  0.1041  


POS 34    W      L      E      N      G      A      E      I      Q      R      T      
          0.1041  0.0909  0.1456  0.0935  0.0935  0.0909  0.1416  0.2385  0.2080  0.1416  0.1322  


POS 45    G      L      E      V      K      P      F      I      T      N      P      
          0.1844  0.2963  0.2820  0.2558  0.1921  0.2167  0.2041  0.1998  0.1921  0.1921  0.1380  


POS 56    R      A      V      K      K      C      T      R      Y      I      D      
          0.0935  0.1495  0.0935  0.1416  0.0935  0.0771  0.1322  0.1416  0.0935  0.0965  0.0464  


POS 67    C      D      L      N      R      I      F      D      L      E      N      
          0.0490  0.0567  0.0542  0.0554  0.0567  0.0935  0.0813  0.0858  0.1292  0.1958  0.1322  


POS 78    L      G      K      K      M      S      E      D      L      P      Y      
          0.2385  0.1732  0.2558  0.1958  0.1878  0.2432  0.2963  0.3184  0.4149  0.3359  0.3399  


POS 89    E      V      R      R      A      Q      E      I      N      H      L      
          0.4116  0.3491  0.2820  0.2913  0.3535  0.3399  0.3456  0.3399  0.4333  0.4078  0.4825  


POS 100    F      G      P      K      D      S      E      D      S      Y      
           0.3992  0.4651  0.4149  0.3578  0.3005  0.2820  0.1878  0.2483  0.2385  0.2385  


POS 110    D      I      I      F      D      L      H      N      T      T      
           0.2963  0.3668  0.3630  0.2865  0.2963  0.2209  0.2122  0.1292  0.0789  0.0441  


POS 120    S      N      M      G      C      T      L      I      L      E      
           0.0771  0.0771  0.1117  0.1635  0.2333  0.2209  0.1878  0.1292  0.0771  0.0858  


POS 130    D      S      R      N      N      F      L      I      Q      M      
           0.0660  0.0336  0.0316  0.0226  0.0102  0.0179  0.0179  0.0327  0.0279  0.0363  


POS 140    F      H      Y      I      K      T      S      L      A      P      
           0.0387  0.0173  0.0218  0.0128  0.0078  0.0044  0.0055  0.0059  0.0055  0.0055  


POS 150    L      P      C      Y      V      Y      L      I      E      H      
           0.0070  0.0167  0.0194  0.0200  0.0387  0.0212  0.0160  0.0157  0.0327  0.0455  


POS 160    P      S      L      K      Y      A      T      T      R      S      
           0.0387  0.0414  0.0279  0.0441  0.0455  0.0884  0.0991  0.1602  0.1635  0.1602  


POS 170    I      A      K      Y      P      V      G      I      E      V      
           0.1088  0.0965  0.1150  0.1878  0.2167  0.3146  0.3535  0.2865  0.2080  0.2080  


POS 180    G      P      Q      P      Q      G      V      L      R      A      
           0.1766  0.2748  0.2333  0.1667  0.2531  0.2385  0.2748  0.2748  0.3630  0.3184  


POS 190    D      I      L      D      Q      M      R      K      M      I      
           0.3146  0.3096  0.2748  0.2292  0.1292  0.1292  0.0744  0.0701  0.1150  0.1117  


POS 200    K      H      A      L      D      F      I      H      H      F      
           0.0723  0.0701  0.1150  0.1732  0.1602  0.1602  0.1205  0.1456  0.1766  0.1532  


POS 210    N      E      G      K      E      F      P      P      C      A      
           0.1958  0.1322  0.1416  0.1178  0.1205  0.1088  0.1205  0.1240  0.1380  0.1322  


POS 220    I      E      V      Y      K      I      I      E      K      V      
           0.1566  0.1698  0.1060  0.1266  0.1178  0.1240  0.2080  0.1766  0.1566  0.2292  


POS 230    D      Y      P      R      D      E      N      G      E      I      
           0.1878  0.2432  0.2041  0.2041  0.2122  0.2122  0.3225  0.3992  0.3005  0.3359  


POS 240    A      A      I      I      H      P      N      L      Q      D      
           0.4149  0.4245  0.5173  0.4078  0.4116  0.4245  0.3359  0.3263  0.3578  0.3399  


POS 250    Q      D      W      K      P      L      H      P      G      D      
           0.4282  0.4825  0.4703  0.4651  0.4600  0.4600  0.3399  0.3578  0.4333  0.4078  


POS 260    P      M      F      L      T      L      D      G      K      T      
           0.3885  0.2913  0.3053  0.3096  0.3184  0.2820  0.3630  0.3005  0.2657  0.1998  


POS 270    I      P      L      G      G      D      C      T      V      Y      
           0.1205  0.1205  0.1041  0.1018  0.1117  0.1150  0.1844  0.1380  0.1117  0.0701  


POS 280    P      V      F      V      N      E      A      A      Y      Y      
           0.0425  0.0744  0.0567  0.0909  0.0965  0.0744  0.0387  0.0464  0.0441  0.0607  


POS 290    E      K      K      E      A      F      A      K      T      T      
           0.0991  0.0771  0.0660  0.1041  0.0935  0.0935  0.0660  0.0832  0.1041  0.1041  


POS 300    K      L      T      L      N      A      K      S      I      R      
           0.1698  0.1041  0.0660  0.0441  0.0405  0.0701  0.1602  0.2333  0.2865  0.3456  


POS 310    C      C      L      H      
           0.4037  0.4556  0.5802  0.6334  


Structured Regions

Aspa iupred3.png

IUPRED predicts one structured region comprised of the whole input sequence.


Results

IUPRED predicts no significant disorder in Aspartoacyclase. The disorder tendency stays below 0.5 in all cases (except for short stretches of about 3-5 residues at each end of the sequence in short disorder mode, which are negligible) and the structured regions mode predicts one continuous structured region spanning all of the protein sequence. This makes sense when looking at the 3D structure: Aspartoacyclase is a rather densely packed globular structure, which according to the assumptions that IUPRED makes has a strong tendency to form many inter-residue contacts and to stabilize itself thereby, markedly reducing the tendency for disorder in the process.

Meta-Disorder

Meta-Disorder, as the name implies, employs a set of so-called orthogonal disorder predictors in order to combine their strengths and mitigate their weak points. It was published in 2009 by Avner Schlessinger, Marco Punta, Guy Yachdav, Laszlo Kajan and Burkhard Rost.

Reference: Paper

As with the previous methods, Meta-Disorder predicts disorder from the amino acid sequence alone; results from the predictors IUPRED, DISOPRED, NORSnet and Ucon are molded into one final result using a neural network.

Results for Aspartoacyclase:

Number Residue NORSnet NORS2st PROFbval bval2st Ucon Ucon2st MD_raw   MD_rel  MD2st 
    1	M	0.33	-	0.99	D	0.17	-	0.551	1	D
    2	T	0.26	-	0.78	D	0.25	-	0.531	0	D
    3	S	0.16	-	0.72	D	0.35	-	0.535	0	D
    4	C	0.23	-	0.65	D	0.33	-	0.505	0	-
    5	H	0.20	-	0.48	D	0.25	-	0.475	1	-
    6	I	0.16	-	0.55	D	0.30	-	0.465	1	-
    7	A	0.34	-	0.56	D	0.40	-	0.444	2	-
    8	E	0.28	-	0.67	D	0.30	-	0.424	3	-
    9	E	0.21	-	0.73	D	0.38	-	0.404	3	-
   10	H	0.15	-	0.70	D	0.30	-	0.374	4	-
   11	I	0.15	-	0.59	D	0.29	-	0.354	5	-
   12	Q	0.15	-	0.60	D	0.28	-	0.313	6	-
   13	K	0.14	-	0.51	D	0.23	-	0.263	8	-
   14	V	0.14	-	0.30	-	0.19	-	0.253	8	-
   15	A	0.16	-	0.24	-	0.19	-	0.250	9	-
   16	I	0.13	-	0.20	-	0.24	-	0.242	9	-
   17	F	0.10	-	0.13	-	0.23	-	0.250	9	-
   18	G	0.13	-	0.18	-	0.21	-	0.242	9	-
   19	G	0.10	-	0.24	-	0.20	-	0.253	8	-
   20	T	0.07	-	0.34	-	0.20	-	0.253	8	-
   21	H	0.06	-	0.26	-	0.26	-	0.260	8	-
   22	G	0.06	-	0.39	-	0.29	-	0.253	8	-
   23	N	0.06	-	0.48	D	0.22	-	0.250	9	-
   24	E	0.06	-	0.47	D	0.18	-	0.242	9	-
   25	L	0.11	-	0.43	-	0.16	-	0.242	9	-
   26	T	0.12	-	0.39	-	0.20	-	0.253	8	-
   27	G	0.10	-	0.32	-	0.20	-	0.242	9	-
   28	V	0.08	-	0.28	-	0.15	-	0.242	9	-
   29	F	0.12	-	0.35	-	0.13	-	0.242	9	-
   30	L	0.14	-	0.28	-	0.15	-	0.242	9	-
   31	V	0.09	-	0.30	-	0.16	-	0.253	8	-
   32	K	0.07	-	0.40	-	0.16	-	0.263	8	-
   33	H	0.06	-	0.40	-	0.18	-	0.293	7	-
   34	W	0.08	-	0.38	-	0.29	-	0.273	8	-
   35	L	0.09	-	0.45	-	0.30	-	0.283	7	-
   36	E	0.09	-	0.56	D	0.41	-	0.313	6	-
   37	N	0.12	-	0.62	D	0.32	-	0.313	6	-
   38	G	0.16	-	0.62	D	0.35	-	0.330	6	-
   39	A	0.11	-	0.64	D	0.46	-	0.313	6	-
   40	E	0.10	-	0.66	D	0.47	-	0.323	6	-
   41	I	0.09	-	0.65	D	0.47	-	0.323	6	-
   42	Q	0.10	-	0.64	D	0.36	-	0.293	7	-
   43	R	0.09	-	0.61	D	0.50	-	0.273	8	-
   44	T	0.08	-	0.61	D	0.56	-	0.273	8	-
   45	G	0.08	-	0.53	D	0.34	-	0.263	8	-
   46	L	0.09	-	0.43	-	0.35	-	0.260	8	-
   47	E	0.10	-	0.33	-	0.32	-	0.253	8	-
   48	V	0.07	-	0.23	-	0.32	-	0.250	9	-
   49	K	0.06	-	0.17	-	0.34	-	0.253	8	-
   50	P	0.08	-	0.18	-	0.37	-	0.263	8	-
   51	F	0.08	-	0.17	-	0.49	-	0.273	8	-
   52	I	0.07	-	0.21	-	0.33	-	0.273	8	-
   53	T	0.06	-	0.28	-	0.53	-	0.303	7	-
   54	N	0.07	-	0.28	-	0.53	-	0.303	7	-
   55	P	0.09	-	0.36	-	0.37	-	0.313	6	-
   56	R	0.08	-	0.41	-	0.51	-	0.313	6	-
   57	A	0.10	-	0.40	-	0.66	D	0.280	7	-
   58	V	0.13	-	0.40	-	0.51	-	0.263	8	-
   59	K	0.16	-	0.48	D	0.37	-	0.263	8	-
   60	K	0.19	-	0.47	D	0.40	-	0.263	8	-
   61	C	0.18	-	0.47	D	0.29	-	0.253	8	-
   62	T	0.16	-	0.55	D	0.35	-	0.263	8	-
   63	R	0.18	-	0.51	D	0.31	-	0.253	8	-
   64	Y	0.22	-	0.47	D	0.25	-	0.273	8	-
   65	I	0.23	-	0.47	D	0.20	-	0.260	8	-
   66	D	0.23	-	0.56	D	0.21	-	0.263	8	-
   67	C	0.25	-	0.57	D	0.16	-	0.263	8	-
   68	D	0.30	-	0.43	-	0.18	-	0.263	8	-
   69	L	0.29	-	0.40	-	0.18	-	0.260	8	-
   70	N	0.28	-	0.40	-	0.25	-	0.263	8	-
   71	R	0.40	-	0.39	-	0.23	-	0.273	8	-
   72	I	0.46	-	0.43	-	0.22	-	0.280	7	-
   73	F	0.46	-	0.37	-	0.19	-	0.273	8	-
   74	D	0.37	-	0.46	-	0.32	-	0.310	6	-
   75	L	0.33	-	0.57	D	0.40	-	0.390	4	-
   76	E	0.36	-	0.61	D	0.30	-	0.444	2	-
   77	N	0.44	-	0.62	D	0.41	-	0.465	1	-
   78	L	0.38	-	0.66	D	0.65	D	0.531	0	D
   79	G	0.30	-	0.70	D	0.64	D	0.485	1	-
   80	K	0.35	-	0.69	D	0.64	D	0.515	0	-
   81	K	0.23	-	0.69	D	0.59	D	0.475	1	-
   82	M	0.23	-	0.66	D	0.42	-	0.444	2	-
   83	S	0.28	-	0.69	D	0.64	D	0.449	2	-
   84	E	0.34	-	0.72	D	0.56	-	0.485	1	-
   85	D	0.29	-	0.74	D	0.45	-	0.424	3	-
   86	L	0.20	-	0.64	D	0.35	-	0.424	3	-
   87	P	0.20	-	0.64	D	0.45	-	0.404	3	-
   88	Y	0.17	-	0.55	D	0.46	-	0.384	4	-
   89	E	0.14	-	0.50	D	0.46	-	0.364	5	-
   90	V	0.13	-	0.45	-	0.30	-	0.333	6	-
   91	R	0.12	-	0.43	-	0.43	-	0.320	6	-
   92	R	0.11	-	0.40	-	0.36	-	0.293	7	-
   93	A	0.11	-	0.34	-	0.36	-	0.283	7	-
   94	Q	0.10	-	0.45	-	0.22	-	0.290	7	-
   95	E	0.12	-	0.41	-	0.25	-	0.303	7	-
   96	I	0.09	-	0.34	-	0.26	-	0.283	7	-
   97	N	0.11	-	0.40	-	0.33	-	0.313	6	-
   98	H	0.10	-	0.49	D	0.39	-	0.313	6	-
   99	L	0.10	-	0.47	D	0.38	-	0.313	6	-
  100	F	0.13	-	0.47	D	0.38	-	0.293	7	-
  101	G	0.14	-	0.54	D	0.58	D	0.323	6	-
  102	P	0.13	-	0.61	D	0.58	D	0.333	6	-
  103	K	0.13	-	0.60	D	0.47	-	0.323	6	-
  104	D	0.11	-	0.61	D	0.71	D	0.323	6	-
  105	S	0.10	-	0.65	D	0.73	D	0.283	7	-
  106	E	0.10	-	0.70	D	0.62	D	0.283	7	-
  107	D	0.12	-	0.70	D	0.42	-	0.273	8	-
  108	S	0.11	-	0.64	D	0.37	-	0.270	8	-
  109	Y	0.12	-	0.50	D	0.23	-	0.253	8	-
  110	D	0.13	-	0.39	-	0.20	-	0.242	9	-
  111	I	0.16	-	0.29	-	0.18	-	0.240	9	-
  112	I	0.15	-	0.20	-	0.16	-	0.240	9	-
  113	F	0.14	-	0.20	-	0.16	-	0.240	9	-
  114	D	0.17	-	0.21	-	0.20	-	0.242	9	-
  115	L	0.21	-	0.20	-	0.19	-	0.253	8	-
  116	H	0.17	-	0.28	-	0.19	-	0.273	8	-
  117	N	0.11	-	0.48	D	0.23	-	0.283	7	-
  118	T	0.13	-	0.39	-	0.24	-	0.283	7	-
  119	T	0.13	-	0.41	-	0.21	-	0.273	8	-
  120	S	0.15	-	0.46	-	0.21	-	0.273	8	-
  121	N	0.22	-	0.54	D	0.18	-	0.263	8	-
  122	M	0.25	-	0.51	D	0.14	-	0.260	8	-
  123	G	0.30	-	0.51	D	0.16	-	0.253	8	-
  124	C	0.26	-	0.42	-	0.18	-	0.250	9	-
  125	T	0.29	-	0.40	-	0.18	-	0.242	9	-
  126	L	0.24	-	0.34	-	0.18	-	0.253	8	-
  127	I	0.17	-	0.28	-	0.23	-	0.260	8	-
  128	L	0.13	-	0.28	-	0.25	-	0.263	8	-
  129	E	0.14	-	0.41	-	0.24	-	0.253	8	-
  130	D	0.14	-	0.54	D	0.18	-	0.253	8	-
  131	S	0.10	-	0.59	D	0.19	-	0.273	8	-
  132	R	0.07	-	0.68	D	0.27	-	0.280	7	-
  133	N	0.05	-	0.64	D	0.28	-	0.273	8	-
  134	N	0.06	-	0.61	D	0.18	-	0.273	8	-
  135	F	0.07	-	0.53	D	0.15	-	0.260	8	-
  136	L	0.08	-	0.47	D	0.13	-	0.242	9	-
  137	I	0.10	-	0.47	D	0.13	-	0.242	9	-
  138	Q	0.16	-	0.42	-	0.13	-	0.242	9	-
  139	M	0.15	-	0.34	-	0.13	-	0.242	9	-
  140	F	0.11	-	0.32	-	0.14	-	0.250	9	-
  141	H	0.13	-	0.41	-	0.14	-	0.263	8	-
  142	Y	0.16	-	0.36	-	0.16	-	0.263	8	-
  143	I	0.12	-	0.34	-	0.16	-	0.263	8	-
  144	K	0.11	-	0.46	-	0.15	-	0.283	7	-
  145	T	0.07	-	0.54	D	0.20	-	0.273	8	-
  146	S	0.07	-	0.55	D	0.17	-	0.253	8	-
  147	L	0.09	-	0.56	D	0.17	-	0.242	9	-
  148	A	0.10	-	0.57	D	0.17	-	0.250	9	-
  149	P	0.09	-	0.60	D	0.13	-	0.253	8	-
  150	L	0.11	-	0.51	D	0.13	-	0.242	9	-
  151	P	0.13	-	0.44	-	0.14	-	0.242	9	-
  152	C	0.12	-	0.38	-	0.13	-	0.240	9	-
  153	Y	0.13	-	0.31	-	0.13	-	0.240	9	-
  154	V	0.18	-	0.28	-	0.13	-	0.242	9	-
  155	Y	0.17	-	0.33	-	0.14	-	0.250	9	-
  156	L	0.21	-	0.47	D	0.13	-	0.253	8	-
  157	I	0.22	-	0.54	D	0.15	-	0.263	8	-
  158	E	0.17	-	0.58	D	0.15	-	0.283	7	-
  159	H	0.16	-	0.62	D	0.17	-	0.303	7	-
  160	P	0.13	-	0.65	D	0.21	-	0.323	6	-
  161	S	0.14	-	0.59	D	0.29	-	0.303	7	-
  162	L	0.17	-	0.58	D	0.41	-	0.303	7	-
  163	K	0.21	-	0.56	D	0.36	-	0.293	7	-
  164	Y	0.32	-	0.51	D	0.29	-	0.273	8	-
  165	A	0.31	-	0.47	D	0.26	-	0.273	8	-
  166	T	0.28	-	0.45	-	0.32	-	0.273	8	-
  167	T	0.22	-	0.41	-	0.33	-	0.273	8	-
  168	R	0.15	-	0.47	D	0.26	-	0.273	8	-
  169	S	0.14	-	0.47	D	0.28	-	0.280	7	-
  170	I	0.12	-	0.46	-	0.29	-	0.273	8	-
  171	A	0.12	-	0.47	D	0.22	-	0.283	7	-
  172	K	0.11	-	0.58	D	0.27	-	0.290	7	-
  173	Y	0.13	-	0.47	D	0.20	-	0.263	8	-
  174	P	0.11	-	0.38	-	0.19	-	0.253	8	-
  175	V	0.10	-	0.26	-	0.26	-	0.250	9	-
  176	G	0.09	-	0.24	-	0.31	-	0.250	9	-
  177	I	0.13	-	0.33	-	0.25	-	0.250	9	-
  178	E	0.20	-	0.28	-	0.37	-	0.253	8	-
  179	V	0.26	-	0.41	-	0.33	-	0.253	8	-
  180	G	0.20	-	0.45	-	0.33	-	0.270	8	-
  181	P	0.17	-	0.59	D	0.25	-	0.283	7	-
  182	Q	0.12	-	0.49	D	0.35	-	0.283	7	-
  183	P	0.12	-	0.51	D	0.28	-	0.273	8	-
  184	Q	0.13	-	0.54	D	0.42	-	0.273	8	-
  185	G	0.10	-	0.51	D	0.33	-	0.263	8	-
  186	V	0.12	-	0.55	D	0.22	-	0.253	8	-
  187	L	0.17	-	0.54	D	0.24	-	0.253	8	-
  188	R	0.14	-	0.48	D	0.24	-	0.263	8	-
  189	A	0.11	-	0.53	D	0.18	-	0.273	8	-
  190	D	0.11	-	0.51	D	0.19	-	0.273	8	-
  191	I	0.08	-	0.41	-	0.31	-	0.283	7	-
  192	L	0.07	-	0.42	-	0.33	-	0.263	8	-
  193	D	0.06	-	0.47	D	0.24	-	0.273	8	-
  194	Q	0.08	-	0.45	-	0.33	-	0.270	8	-
  195	M	0.04	-	0.34	-	0.26	-	0.263	8	-
  196	R	0.04	-	0.43	-	0.34	-	0.273	8	-
  197	K	0.05	-	0.44	-	0.34	-	0.263	8	-
  198	M	0.06	-	0.29	-	0.34	-	0.263	8	-
  199	I	0.06	-	0.28	-	0.22	-	0.253	8	-
  200	K	0.07	-	0.34	-	0.22	-	0.263	8	-
  201	H	0.07	-	0.32	-	0.20	-	0.253	8	-
  202	A	0.08	-	0.28	-	0.15	-	0.250	9	-
  203	L	0.08	-	0.35	-	0.15	-	0.253	8	-
  204	D	0.09	-	0.43	-	0.19	-	0.263	8	-
  205	F	0.11	-	0.41	-	0.18	-	0.263	8	-
  206	I	0.12	-	0.45	-	0.18	-	0.253	8	-
  207	H	0.15	-	0.59	D	0.23	-	0.270	8	-
  208	H	0.18	-	0.59	D	0.40	-	0.290	7	-
  209	F	0.22	-	0.58	D	0.24	-	0.283	7	-
  210	N	0.27	-	0.63	D	0.37	-	0.293	7	-
  211	E	0.27	-	0.66	D	0.53	-	0.313	6	-
  212	G	0.28	-	0.68	D	0.44	-	0.313	6	-
  213	K	0.26	-	0.70	D	0.46	-	0.323	6	-
  214	E	0.26	-	0.71	D	0.50	-	0.323	6	-
  215	F	0.20	-	0.70	D	0.56	-	0.303	7	-
  216	P	0.21	-	0.69	D	0.37	-	0.293	7	-
  217	P	0.24	-	0.69	D	0.28	-	0.280	7	-
  218	C	0.14	-	0.66	D	0.28	-	0.263	8	-
  219	A	0.14	-	0.58	D	0.19	-	0.263	8	-
  220	I	0.15	-	0.52	D	0.19	-	0.263	8	-
  221	E	0.11	-	0.47	D	0.22	-	0.270	8	-
  222	V	0.11	-	0.34	-	0.26	-	0.273	8	-
  223	Y	0.12	-	0.30	-	0.28	-	0.280	7	-
  224	K	0.08	-	0.37	-	0.34	-	0.280	7	-
  225	I	0.09	-	0.32	-	0.33	-	0.273	8	-
  226	I	0.07	-	0.35	-	0.29	-	0.283	7	-
  227	E	0.09	-	0.43	-	0.38	-	0.313	6	-
  228	K	0.09	-	0.49	D	0.61	D	0.333	6	-
  229	V	0.12	-	0.49	D	0.58	D	0.337	6	-
  230	D	0.16	-	0.53	D	0.75	D	0.354	5	-
  231	Y	0.14	-	0.52	D	0.84	D	0.343	5	-
  232	P	0.12	-	0.57	D	0.84	D	0.313	6	-
  233	R	0.13	-	0.66	D	0.59	D	0.303	7	-
  234	D	0.15	-	0.69	D	0.70	D	0.310	6	-
  235	E	0.10	-	0.71	D	0.59	D	0.293	7	-
  236	N	0.12	-	0.71	D	0.62	D	0.303	7	-
  237	G	0.17	-	0.67	D	0.44	-	0.293	7	-
  238	E	0.22	-	0.60	D	0.40	-	0.283	7	-
  239	I	0.17	-	0.53	D	0.36	-	0.270	8	-
  240	A	0.16	-	0.38	-	0.30	-	0.260	8	-
  241	A	0.19	-	0.29	-	0.22	-	0.253	8	-
  242	I	0.16	-	0.28	-	0.24	-	0.263	8	-
  243	I	0.22	-	0.33	-	0.24	-	0.263	8	-
  244	H	0.25	-	0.34	-	0.34	-	0.293	7	-
  245	P	0.14	-	0.48	D	0.41	-	0.323	6	-
  246	N	0.16	-	0.53	D	0.30	-	0.343	5	-
  247	L	0.16	-	0.58	D	0.53	-	0.343	5	-
  248	Q	0.16	-	0.61	D	0.71	D	0.374	4	-
  249	D	0.22	-	0.64	D	0.59	D	0.354	5	-
  250	Q	0.30	-	0.64	D	0.51	-	0.364	5	-
  251	D	0.34	-	0.62	D	0.52	-	0.333	6	-
  252	W	0.33	-	0.52	D	0.65	D	0.313	6	-
  253	K	0.22	-	0.58	D	0.68	D	0.283	7	-
  254	P	0.21	-	0.58	D	0.63	D	0.283	7	-
  255	L	0.18	-	0.54	D	0.45	-	0.263	8	-
  256	H	0.16	-	0.68	D	0.27	-	0.263	8	-
  257	P	0.18	-	0.69	D	0.28	-	0.273	8	-
  258	G	0.19	-	0.57	D	0.21	-	0.270	8	-
  259	D	0.28	-	0.54	D	0.16	-	0.290	7	-
  260	P	0.25	-	0.54	D	0.23	-	0.270	8	-
  261	M	0.19	-	0.40	-	0.24	-	0.273	8	-
  262	F	0.16	-	0.34	-	0.29	-	0.253	8	-
  263	L	0.13	-	0.37	-	0.30	-	0.253	8	-
  264	T	0.10	-	0.46	-	0.20	-	0.242	9	-
  265	L	0.14	-	0.56	D	0.20	-	0.253	8	-
  266	D	0.13	-	0.61	D	0.20	-	0.263	8	-
  267	G	0.11	-	0.62	D	0.26	-	0.280	7	-
  268	K	0.10	-	0.60	D	0.34	-	0.283	7	-
  269	T	0.10	-	0.60	D	0.40	-	0.273	8	-
  270	I	0.08	-	0.46	-	0.41	-	0.250	9	-
  271	P	0.07	-	0.43	-	0.35	-	0.250	9	-
  272	L	0.12	-	0.46	-	0.29	-	0.242	9	-
  273	G	0.10	-	0.53	D	0.18	-	0.242	9	-
  274	G	0.08	-	0.52	D	0.19	-	0.250	9	-
  275	D	0.05	-	0.62	D	0.19	-	0.253	8	-
  276	C	0.06	-	0.68	D	0.15	-	0.263	8	-
  277	T	0.10	-	0.59	D	0.16	-	0.263	8	-
  278	V	0.08	-	0.52	D	0.17	-	0.263	8	-
  279	Y	0.09	-	0.33	-	0.20	-	0.242	9	-
  280	P	0.10	-	0.27	-	0.17	-	0.242	9	-
  281	V	0.12	-	0.23	-	0.21	-	0.242	9	-
  282	F	0.12	-	0.18	-	0.17	-	0.253	8	-
  283	V	0.09	-	0.24	-	0.16	-	0.263	8	-
  284	N	0.05	-	0.28	-	0.23	-	0.303	7	-
  285	E	0.06	-	0.39	-	0.28	-	0.384	4	-
  286	A	0.09	-	0.35	-	0.46	-	0.404	3	-
  287	A	0.08	-	0.43	-	0.72	D	0.418	3	-
  288	Y	0.08	-	0.37	-	0.79	D	0.374	4	-
  289	Y	0.09	-	0.55	D	0.61	D	0.354	5	-
  290	E	0.10	-	0.41	-	0.49	-	0.333	6	-
  291	K	0.10	-	0.50	D	0.65	D	0.323	6	-
  292	K	0.07	-	0.47	D	0.66	D	0.323	6	-
  293	E	0.07	-	0.36	-	0.79	D	0.333	6	-
  294	A	0.06	-	0.29	-	0.95	D	0.354	5	-
  295	F	0.08	-	0.27	-	0.82	D	0.333	6	-
  296	A	0.09	-	0.32	-	0.70	D	0.323	6	-
  297	K	0.09	-	0.42	-	0.41	-	0.343	5	-
  298	T	0.08	-	0.42	-	0.36	-	0.343	5	-
  299	T	0.10	-	0.51	D	0.36	-	0.414	3	-
  300	K	0.09	-	0.54	D	0.64	D	0.455	2	-
  301	L	0.09	-	0.48	D	0.70	D	0.394	4	-
  302	T	0.15	-	0.55	D	0.43	-	0.404	3	-
  303	L	0.15	-	0.48	D	0.46	-	0.374	4	-
  304	N	0.12	-	0.48	D	0.34	-	0.374	4	-
  305	A	0.13	-	0.47	D	0.19	-	0.374	4	-
  306	K	0.22	-	0.55	D	0.19	-	0.384	4	-
  307	S	0.07	-	0.53	D	0.18	-	0.434	2	-
  308	I	0.07	-	0.41	-	0.23	-	0.424	3	-
  309	R	0.07	-	0.37	-	0.21	-	0.414	3	-
  310	C	0.11	-	0.60	D	0.19	-	0.414	3	-
  311	C	0.14	-	0.67	D	0.14	-	0.394	4	-
  312	L	0.15	-	0.72	D	0.13	-	0.424	3	-
  313	H	0.44	-	0.80	D	0.13	-	0.485	1	-


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


The last column indicates whether or not disorder was predicted at the current position. Meta-Disorder predicts a total of four disorder positions, which are not significant. This coincides with the predictions of the other programs employed previously - not alltogether surprising, since Meta-Disorder draws its predictions from two of them.

Prediction of transmembrane alpha-helices and signal peptides

The results of this task are unequivocal: Aspartoacyclase does not contain any transmembrane regions. From a biological point of view this was to be expected, as Aspartoacyclase is known to be located in the cytosol.

TMHMM

Since the VM version could not be made to work, we used the server at http://www.cbs.dtu.dk/services/TMHMM/.

TMHMM uses a hidden markov model to predict transmembrane helices in proteins. It was published in 1998 by E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.

Reference: Original paper

The hidden markov model used by TMHMM models the biological structure with states for helix turns, helix caps and loops on either side of the membrane, which are specially designed to model membrane insertion, too. The HMM probabilities were estimated both by using a maximum likelihood method and a discriminative method.

Results for Aspartoacyclase very clearly show absence of any sort of transmembrane structure, which is biologically sound.

Sp P45381 ACY2 HUMAN.gif

# sp_P45381_ACY2_HUMAN Length: 313
# sp_P45381_ACY2_HUMAN Number of predicted TMHs:  0
# sp_P45381_ACY2_HUMAN Exp number of AAs in TMHs: 0.2005
# sp_P45381_ACY2_HUMAN Exp number, first 60 AAs:  0.01618
# sp_P45381_ACY2_HUMAN Total prob of N-in:        0.03827
sp_P45381_ACY2_HUMAN	TMHMM2.0	outside	     1   313

http://www.cbs.dtu.dk/services/TMHMM-2.0/TMHMM2.0.guide.html#output

Phobius & PolyPhobius

Aspa phobius.png

OCTOPUS & SPOCTOPUS

No transmembrane regions were predicted by both methods.

SignalP

HMM

ASPA Plot.hmm.1.gif

Neural Network

ASPA Plot.nn.1.gif

TargetP

### 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_P45381_ACY2_HUMAN  313          0.073  0.109  0.898   _    2
----------------------------------------------------------------------
cutoff                             0.000  0.000  0.000

http://www.cbs.dtu.dk/services/TargetP-1.1/output.php

Prediction of GO terms

GOPET

GOid Aspect Confidence GO Term
GO:0016787 F 96% hydrolase activity
GO:0004046 F 82% aminoacyclase activity
GO:0019807 F 82% aspartoacyclase activity
GO:0016788 F 81% hydrolase activity acting on ester bonds

Pfam

Aspa pfam significant.png

ProtFun 2.2

############## ProtFun 2.2 predictions ##############

>sp_P45381_A

# Functional category                  Prob     Odds
  Amino_acid_biosynthesis              0.071    3.233
  Biosynthesis_of_cofactors            0.144    2.003
  Cell_envelope                        0.033    0.535
  Cellular_processes                   0.137    1.875
  Central_intermediary_metabolism   => 0.334    5.309
  Energy_metabolism                    0.226    2.511
  Fatty_acid_metabolism                0.022    1.663
  Purines_and_pyrimidines              0.367    1.512
  Regulatory_functions                 0.021    0.128
  Replication_and_transcription        0.167    0.625
  Translation                          0.113    2.559
  Transport_and_binding                0.017    0.042

# Enzyme/nonenzyme                     Prob     Odds
  Enzyme                            => 0.703    2.454
  Nonenzyme                            0.297    0.416

# Enzyme class                         Prob     Odds
  Oxidoreductase (EC 1.-.-.-)          0.111    0.534
  Transferase    (EC 2.-.-.-)          0.202    0.585
  Hydrolase      (EC 3.-.-.-)          0.115    0.363
  Lyase          (EC 4.-.-.-)          0.031    0.662
  Isomerase      (EC 5.-.-.-)       => 0.084    2.637
  Ligase         (EC 6.-.-.-)          0.074    1.460

# Gene Ontology category               Prob     Odds
  Signal_transducer                    0.053    0.246
  Receptor                             0.004    0.024
  Hormone                              0.001    0.206
  Structural_protein                   0.001    0.041
  Transporter                          0.025    0.230
  Ion_channel                          0.015    0.257
  Voltage-gated_ion_channel            0.004    0.173
  Cation_channel                       0.011    0.234
  Transcription                        0.100    0.785
  Transcription_regulation             0.039    0.313
  Stress_response                      0.010    0.117
  Immune_response                      0.061    0.720
  Growth_factor                        0.006    0.450
  Metal_ion_transport                  0.009    0.020