Secondary Structure Prediction

PSIPRED

PSIPRED delivers many different kind of output file formats. The pictures show the pdf-output which shows the secondary structure in a graphical kind. It predicts 14 alpha-helices and 15 beta-sheets. The rest are predicted coils.

First part of the PSIPRED output

Second part of the PSIPRED output

Legend for the PSIPRED output

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Jpred3

The following alignemt shows the output of Jpred3. The secondary structure elements is marked by ourself. It predicted 14 alpha-helices and 15 beta-sheets.

Jpred output with colored secondary structure elements

DSSP

We started DSSP on the webserver with the PDBB-id. Therefore, we get the secondary structure assignment for the whole protein and not only for the alpha-subunit. The following sequence with the according secondary structure is the output for our sequence (we extracted it from the whole). It assigned 16 alpha-helices and no beta-sheet.

                    10        20        30        40        50
                     |         |         |         |         |
   1 -   52 LWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFG
   1 -   52   T  TT    T      TTT      TT TT TT HHHHHHHHHHHHHHH
   1 -   52    * ** *                     *
   1 -   52    A  AAAA AAA   A AA A A  AA   AAA        AA  A   A

                  60        70        80        90       100       110
                   |         |         |         |         |         |
  53 -  112 TLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWK
  53 -  112       SSSSTT   TTT   TT    SSSSSTTT SSSSSTTHHHHHHHHHHHHHHSSS
  53 -  112           * ***
  53 -  112 AA AA A   AAAA  AAA A A A   A    AAA A A A                AA
                 120       130       140       150       160       170
                   |         |         |         |         |         |
 113 -  172 SAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDD
 113 -  172  TT  SSS  SSSSS  T TSSSSSSSTTTT   HHHHHHHHHHHHHTT  SSSSS   T
 113 -  172
 113 -  172  AA      A A A A A A             AAA  AA                   A
                 180       190       200       210       220       230
                   |         |         |         |         |         |
 173 -  232 PSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGP
 173 -  232 T      TT THHHHHHTT TTTT   HHHHHHHHHHHHHTT SSSSS   TTT TTTTT
 173 -  232
 173 -  232 A      AAA A  AA  A A A    A   AA  AA                  A   A
                 240       250       260       270       280       290
                   |         |         |         |         |         |
 233 -  292 GIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGDEVDFTC
 233 -  292 TTTT SSSSSTTTTSSSSSSSS TT HHHHHHHHHHHHHHHHH  TTSSS    T  THH
 233 -  292
 233 -  292   AA   A AAAAAAAAAA      AAA  A   A  A   AA A A       A AAA
                 300       310       320       330       340       350
                   |         |         |         |         |         |
 293 -  352 WKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTI
 293 -  352 HHH HHHHHHHHHHT TT THHHHHHHHHHHHHHHHTTT SSSSSHHHHHTT    TT S
 293 -  352         *  ****  *
 293 -  352  AA AA AAA AAAAAAAA AA   A  AA  A  AAAA         A  A A AAA
                 360       370       380       390       400       410
                   |         |         |         |         |         |
 353 -  412 IQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYGPDWKDFYVVEPLAFEGTPEQ
 353 -  412 SSS  TTTTT HHHHHHHHHHTT SSSS TT  TTT  TT THHHHHH  TT TT  HHH
 353 -  412       *
 353 -  412    AAAAAAAAAAA   A  AAA A          A AA A  AA  A   AA A AAA
                 420       430       440       450       460       470
                   |         |         |         |         |         |
 413 -  472 KALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKLTSDLTFAYERLSHFRCELL
 413 -  472 HTTSSSSSSSS TTT TTTTHHHHHTTHHHHHHHHHHT TT   HHHHHHHHHHHHHHHH
 413 -  472                                       * **
 413 -  472 AAA              A   A                AAA AAAAA AA   A  AA
                 480       490
                   |         |
 473 -  492 RRGVQAQPLNVGFCEQEFEQ
 473 -  492 HTT     TTT   TT
 473 -  492
 473 -  492 A A A    AA A AA  AA

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