TMpred

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Contents

Description

TMpred makes a prediction of membrane-spanning regions and their orientation [1]. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring.

Website

http://www.ch.embnet.org/software/TMPRED_form.html

Example

Input

>MY_PROTEIN_SEQ 
MKSAFSFLPNWPLAPDAIFWAGFALFAAGLCGELCYRAWRLPRITGYAVIGLVAGSFGFGVIDASTDDTSRLLVNVALGL
LLFELGSRLDLRWIRRNPWLIASSLAEATLTFVLVLAVLLLLKVPGMIALVLAAIAISTSPAMVIQLKTELRAEGQVSQR
LITLSALNSVYAVVLTKLVTSWLHQEAYGNVFATILQPIYLLAGSFIVAYLFARACNYLFRHVAATMRDEHSFVALFGLV
VLAIAVAQVLKLSTMLTLLLAGIIVKNLEARPQLWPEHFGTAGWLLTVILFVLTLTSFEGQDIAAGGLIAGALIATRFLA
KLVGVLAFAKPSGLGVKQGIALGVSLVPMSALAYLLVDDTYQLYPNFDPRLRAVVMCSIVVLQLIGPLVVYRSLSAVGER 
RDAS

Output

TMpred prediction output for : MY_PROTEIN_SEQ
 
Sequence: MKS...DAS   length:     404
Prediction parameters: TM-helix length between 17 and 33
 
 
1.) Possible transmembrane helices
==================================
The sequence positions in brackets denominate the core region.
Only scores above  500 are considered significant.
 
Inside to outside helices :  11 found
      from        to    score center
  17 (  17)  36 (  36)   1906     28
  44 (  46)  62 (  62)   1681     54
  71 (  71)  87 (  87)    296     79
 124 ( 124) 145 ( 143)   2130    134
 161 ( 163) 179 ( 179)    923    171
 192 ( 194) 216 ( 210)   1696    202
 232 ( 234) 250 ( 250)   1803    242
 278 ( 278) 298 ( 296)   1883    288
 303 ( 305) 323 ( 321)    901    313
 339 ( 339) 357 ( 357)   1372    347
 373 ( 373) 391 ( 389)   1886    381

Outside to inside helices :  11 found
      from        to    score center
  17 (  17)  36 (  36)   2206     26
  44 (  46)  62 (  62)   1731     54
  72 (  72)  91 (  91)    838     82
 124 ( 128) 147 ( 145)   1939    137
 161 ( 161) 179 ( 179)    911    171
 192 ( 194) 213 ( 210)   1893    202
 231 ( 231) 250 ( 250)   2014    242
 279 ( 279) 298 ( 296)   2013    288
 300 ( 300) 320 ( 320)   1237    309
 338 ( 338) 357 ( 354)   1456    346
 371 ( 373) 390 ( 390)   1614    381


 
2.) Table of correspondences
============================
Here is shown, which of the inside->outside helices correspond
to which of the outside->inside helices.
  Helices shown in brackets are considered insignificant.
  A "+"  symbol indicates a preference of this orientation.
  A "++" symbol indicates a strong preference of this orientation.
 
           inside->outside | outside->inside
    17-  36 (20) 1906      |    17-  36 (20) 2206 ++   
    44-  62 (19) 1681      |    44-  62 (19) 1731      
(   71-  87 (17)  296    ) |    72-  91 (20)  838 ++   
   124- 145 (22) 2130  +   |   124- 147 (24) 1939      
   161- 179 (19)  923      |   161- 179 (19)  911      
   192- 216 (25) 1696      |   192- 213 (22) 1893  +   
   232- 250 (19) 1803      |   231- 250 (20) 2014 ++   
   278- 298 (21) 1883      |   279- 298 (20) 2013  +   
   303- 323 (21)  901      |   300- 320 (21) 1237 ++   
   339- 357 (19) 1372      |   338- 357 (20) 1456  +   
   373- 391 (19) 1886 ++   |   371- 390 (20) 1614      


3.) Suggested models for transmembrane topology
===============================================
These suggestions are purely speculative and should be used with
EXTREME CAUTION since they are based on the assumption that
all transmembrane helices have been found.
In most cases, the Correspondence Table shown above or the
prediction plot that is also created should be used for the
topology assignment of unknown proteins.

2 possible models considered, only significant TM-segments used

*** the models differ in the number of TM-helices ! ***

-----> STRONGLY prefered model: N-terminus outside
11 strong transmembrane helices, total score : 17582
 # from   to length score orientation
 1   17   36 (20)    2206 o-i
 2   44   62 (19)    1681 i-o
 3   72   91 (20)     838 o-i
 4  124  145 (22)    2130 i-o
 5  161  179 (19)     911 o-i
 6  192  216 (25)    1696 i-o
 7  231  250 (20)    2014 o-i
 8  278  298 (21)    1883 i-o
 9  300  320 (21)    1237 o-i
10  339  357 (19)    1372 i-o
11  371  390 (20)    1614 o-i

------> alternative model
10 strong transmembrane helices, total score : 16494
 # from   to length score orientation
 1   17   36 (20)    1906 i-o
 2   44   62 (19)    1731 o-i
 3  124  145 (22)    2130 i-o
 4  161  179 (19)     911 o-i
 5  192  216 (25)    1696 i-o
 6  231  250 (20)    2014 o-i
 7  278  298 (21)    1883 i-o
 8  300  320 (21)    1237 o-i
 9  339  357 (19)    1372 i-o
10  371  390 (20)    1614 o-i

References

  1. K. Hofmann & W. Stoffel (1993) TMbase - A database of membrane spanning proteins segments

    Biol. Chem. Hoppe-Seyler 374,166

    [TMpred]
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