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.

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

There are no gaps and the sequences align over the whole length. If the sequences were of different length, the shorter one would have to be padded with gap characters: "-".

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. Given the good, full-length alignment, SwissModel had no problem modeling the entire protein.

Model QMEAN score vs. expected QMean scores of protein structures, as a function of domain size. The model (red cross) is within the lower 2 sigma range in quality for its size.

Cartoon view of the model, colored by QMEAN scores

The target-template alignment:

TARGET    1       AVHVAVYS GVEVYECFIK GVSVMRRRRD SWLNATQILK VADFDKPQRT
1bm8A     4       qiysarys gvdvyefihs tgsimkrkkd dwvnathilk aanfakakrt
                                                                     
TARGET            sssssss   ssssssss   sssssss     ssshhhhh h    hhhhh
1bm8A             sssssss   ssssssss   sssssss     ssshhhhh h    hhhhh


TARGET    49    RVLERQVQIG AHEKVQGGYG KYQGTWVPFQ RGVDLATKYK VDGIMSPILS
1bm8A     52    rilekevlke thekvqggfg kyqgtwvpln iakqlaekfs vydqlkplfd
                                                                     
TARGET          hhhhhh       sss         ssss hh hhhhhhhh    hh   hhhh
1bm8A           hhhhhh       sss         ssss hh hhhhhhhh    hh   hhhh


TARGET    99    L                                                     
1bm8A     102   f-                                                    
                                                                     
TARGET                                                                
1bm8A                           

Local quality estimation: ANOLEA and QMEAN scores as graphical output

Model data

• SCHPO_model.pdb: MBP1_SCHPO APSES domain model coordinates
• Local_energy_profile.csv: Energy scores for the MBP1_SCHPO APSES domain model coordinates