Request returning 1D structure prediction in MSF format
Example for requesting to return the 1D structure prediction in MSF format
Bold face: keyword "return phd msf"
Input (request of you)
Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu
joe@amino.churn.edu
return phd msf
# sh3
KELVLALYDYQEKSPREVTMKKGDILTL
LNSTNKDWWKVEVNDRQGFVPAAYVKKLD
Output (result returned)
- Block with sequence alignment.
- Block with information about prediction method.
- Block with prediction in default format.
- Block with alignment, and prediction in MSF format (shown here):
Explanations:
- 1st block Alignment
- sequence identifier
- residues (in chunks of 60 per line)
- 2nd block Predictions
- AApred : sequence for which structure is predicted
- PHDsec : secondary structure in three states: helix H, strand E, rest L
- RELsec : reliability of secondary structure prediction scaled between 0 (low) and 9 (high)
- SUBsec : subset of the prediction, for all residues with a reliability index RELsec ≥ 4, i.e., a subset for which the expected average accuracy is ≥ 88% (tables)
- P_3acc : residue solvent accessibility in three states: buried b (< 9% relative accessibility), intermediate blank, and exposed e (> 25% relative accessibility)
- RELacc : reliability of accessibility prediction scaled between 0 (low) and 9 (high)
- SUBacc : subset of the prediction, for all residues with a reliability index RELacc ≥ 3, i.e., a subset for which the expected average accuracy is ≥ 90% (tables)
- PHDacc : relative residue solvent accessibility ≤ n**2, i.e., the square of the number given per residue provides a lower limit for the relative accessibility
PHD prediction and alignment in MSF format
....,....1....,....2....,....3....,....4....,....5....,....6
t3_27793 KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
spcn_chick KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
spca_drome KECVVALYDYTEKSPREVSMKKGDVLTLLNSNNKDWWKVEVNDRQGFVPAAYIKKID
foda_mouse ..........................ALLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
spca_human EQRVMALYDFQARSPREVTMKKGDVLTLLSSINKDWWKVEAADHQGIVPAVYVRRL.
blk_human KHFVVALYDYTAMNDRDLQMLKGEKLQVLKGT.GDWWLArvTGREGYVPSNFVARVE
mysd_dicdi KPSAKALYDFDAESSMELSFKEGDILTVLDQSSGDWWDAELKGRRGKVPSNYLQLI.
ps20_yeast .EFARALYDFVPENpmEVALKKGDLMAILSKKdsDWWKVRtnGNIGYIPYNYIEII.
mysc_acaca PEQARALYDFAAENPDELTFNEGAVVTVINKSNPDWWEGELNGQRGVFPASYVELI.
mysb_acaca KPQVKALYDYDAQTGDELTFKEGDTIIVHQKDPAGWWEGELNGKRGWVPANYVQDI.
cc15_schpo .GYVIALYDYQAQIPEEISFQKGDTLMVLRTQEDGWWDGEinSKRGLFPSNFVQTV.
blk_mouse ERFVVALFDYAAVNDRDLQVLKGEKLQVLRST.GDWWLArvTGREGYVPSNFVAPVE
itk_mouse ETLVIALYDYQTNDPQELALRCDEEYYLLDSSEIHWWRVQdnGHEGYAPSSYL....
yha2_yeast ...VRALYDLTTNEPDELSFRKGDVITVLEQVYRDWWKGALRGNMGIFPLNYVTPI.
itk_human ETVVIALYDYQTNDPQELALRRNEEYCLLDSSEIHWWRVQdnGHEGYVPSSYL....
crkl_human .EYVRTLYDFPGNDAEDLPFKKGEILVIIEKPEEQWWSARNKdrVGMIPVPYVEKL.
vav_human .....ARYDFCARDRSELSLKEGDIIKILNKKgqGWWRGEIYGRVGWFPANYVEE..
srcn_mouse .TTFVALYDYESRTETDLSFKKGERLQIVNNTRkdWWLAHstGQTGYIPSNYVAPSD
lyn_human GDIVVALYPYDGIHPDDLSFKKGEKMKVLEEH.GEWWKAklTKKEGFIPSNYVAKLN
fyn_xiphe .TLFVALYDYEARTEDDLSFRKGERFQILNSTEGDWWDARstGGSGYIPSNYVAPVD
fgr_human .TLFIALYDYEARTEDDLTFTKGEKFHILNNTEGDWWEARssGKTGCIPSNYVAPVD
lyn_rat GDIVVALYPYDGIHPDDLSFKKGEKMKVLEEH.GEWWKAKssKREGFIPSNYVAKVN
lyn_mouse GDIVVALYPYDGIHPDDLSFKKGEKMKVLEEH.GEWWKAKssKREGFIPSNYVAKVN
fgr_mouse .TIFVALYDYEARTGDDLTFTKGEKFHILNNTEYDWWEARssGHRGYVPSNYVAPVD
PREDICTIONS:
AApred .ELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
PHDsec . EEEEEEE EEE EEEEE EEE EEE EEE
RELsec .38999982488784212444897899847898332566256983211221221149
SUBsec ..EEEEEE..LLLL.......LLLEEEE.LLLL...EEE.LLLL............L
P_3acc .ebbbbbbebeeeeeeebebeebeebebbeeeeeebbebeeeeeebbbbbebbeebe
RELacc .51739931133514542125503152644544531343225444303313251407
SUBacc .e.b.bb.....e.eee...ee...b.bbeeeee...e...eeee.......b.e.e
PHDacc .70000006077767770607707606007777770070677777000007006709
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