Homology modeling fallback data

Homology Modeling
Fallback Data

Here are results from a homology modeling exercise using SwissModel, as a fallback for technical problems with the assignment i.e network problems or other issues with the program or input data.

   

Target sequence

This is just one of the reference species' sequences - I chose Mbp1_SCHPO because it is the most distantly related to saccharomyces cerevisiae.

>MBP1_SCHPO NP_593032 23..96
IKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATK
YKV

FASTA formatted target-template alignment

This uses the 1BM8 PDB file as template, the sequence was extracted from coordinates using the WhatIf server.

>1BM8_A
QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI
LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF
>Mbp1_SCHPO 2-100 NP_593032
AVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRV
LERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSL

[TBC once the SwissModel server is back...]

SwissModel response

Explanation of the output is found in the SwissModel Help page.

Graphical comparison of template and target sequence to emphasize which regions have been modelled.

Model QMEAN score vs. expected QMean scores of protein structures, as a function of domain size.

Cartoon view of the model, colored by QMEAN scores

The target-template alignment:

TARGET    1                        IK -GVSVMRRRR DSWLNATQIL KVADFDKPQR
1mb1A     3     nqiysarysg vdvyef--ih stgsimkrkk ddwvnathil kaanfakakr
                                                                     
TARGET                                              ssshhhh hh    hhhh
1mb1A            sssssss   ssssss  ss   sssssss     ssshhhh hh    hhhh


TARGET    32    TRVLERQVQI GAHEKVQGGY GKYQGTWVPF QRGVDLATK  ----------
1mb1A     51    trilekevlk ethekvqggf gkyqgtwvpl niakqlaekf svydqlkplf
                                                                     
TARGET          hhhhhhhhh     sss         ssss h hhhhhhhhh            
1mb1A           hhhhh         sss         ssss h hhhhhhhhh    hh   hh 

Local quality estimation: ANOLEA and QMEAN scores as graphical output

Model coordinates

• MBP1_SCHPO APSES domain model coordinates