Secondary Structure Prediction
PSIPRED
PSIPRED delivers many different kind of output file formats. The pictures show the pdf-output (Figure 1 and 2, Figure 3 is the legend) which shows the secondary structure in a graphical kind. It predicts 14 alpha-helices and 15 beta-sheets. The rest are predicted coils.
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Jpred3
The following alignment (Figure 4) shows the output of Jpred3. The secondary structure elements is marked by ourself. It predicted 14 alpha-helices and 15 beta-sheets.
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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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