AlphaFold chain table reports wrong "Seen" residues for fusion proteins

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.3.1-arm64-arm-64bit
ChimeraX Version: 1.4.dev202203271748 (2022-03-27 17:48:18 UTC)
Description
The alphafold match command on structure 7mn5 logs a misleading chain table.  It shows uniprot P0AEX9 which is from the 7mn5 mmcif header has 1% identity and (I think correctly) says 7mn5 includes 366 residues from this sequences but reports 579 residues seen.

I am not sure why the percent identity is 1%.  That indicates some problem.

And the "Seen" column of the table is reporting all residues in the structure for that chain (B) instead of just the residue range that the mmCIF _struct_ref_seq table says belong to this uniprot id.  In other words, the code is not handling mmCIF files where a uniprot id is listed for just part of a chain.  In the 7mn5 case it looks like chain B is a fusion protein.  Or maybe P0AEX9 is just wrong since matchmaker reports 1% sequence identity.

Log:
UCSF ChimeraX version: 1.4.dev202203271748 (2022-03-27)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7mn5 format mmcif fromDatabase pdb

7mn5 title:  
Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain [more
info...]  
  
Chain information for 7mn5 #1  
---  
Chain | Description | UniProt  
A | Receptor tyrosine-protein kinase erbB-3 | ERBB3_HUMAN  
B | Receptor tyrosine-protein kinase erbB-2,Maltose/maltodextrin-binding
periplasmic protein | MALE_ECOLI  
H | Isoform 6 of Pro-neuregulin-1, membrane-bound isoform | NRG1-6_HUMAN  
  
Non-standard residues in 7mn5 #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> alphafold match #1

UniProt identifiers must be 6 or 10 characters long, got "Q02297-6"  

1 UniProt id does not have an AlphaFold database model: Q02297-6 (chain H)  

3 AlphaFold models found using UniProt identifiers: P21860 (chain A), P04626
(chain B), P0AEX9 (chain B)  
1 AlphaFold model found using sequence similarity searches: A0A140LHZ9 (chain
H)  
AlphaFold chains matching 7mn5  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
H | A0A140LHZ9_MOUSE | A0A140LHZ9 | 1.34 | 87 | 49 | 86  
B | ERBB2_HUMAN | P04626 | 3.12 | 1029 | 579 | 100  
A | ERBB3_HUMAN | P21860 | 31.80 | 1021 | 585 | 100  
B | MALE_ECOLI | P0AEX9 | 3.91 | 366 | 579 | 1  
  
Opened 4 AlphaFold models  




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[Tom Goddard]

I think the 1% identity is wrong because the alphafold match command asks MatchMaker to align the alphafold model to the entire chain instead of just the residue range it matches, and that residue range has no structure residues, so matchmaker finds some horrible match to another part of the sequence. I would have expected to find the best sequence match even though there are no structure residues and then fail to make an alignment. But I am not even sure if matchmaker is using the full 7mn5 chain B sequence since the code is being handed only the atoms for that chain.

[Tom Goddard]

The P0AEX9 indeed has high sequence identity (> 90%) to 7mn5 chain B.