Foldseek Query Inconsistency

[yonatan212]

Issue Description

When querying the PDB entry 3k44 using Foldseek, I receive a hit. However, when I query the same against the entire PDB database, including 3k44, I get multiple hits but not for 3k44 itself.

Foldseek Commands Used

Query against a single PDB entry

/content/foldseek/bin/foldseek easy-search q 3k44 aln.m8 tmpFolder
--format-output "query,target,qstart,qend,tstart,tend,alntmscore,qtmscore,evalue,qlen,alnlen,qcov"
--alignment-type 1

Query against the entire PDB database

/content/foldseek/bin/foldseek easy-search q pdb aln.m8 tmpFolder
--format-output "query,target,qstart,qend,tstart,tend,alntmscore,qtmscore,evalue,qlen,alnlen,qcov"
--alignment-type 1

Expected Behavior

When querying against the entire PDB database, I expect to see a hit for 3k44.

Actual Behavior

A hit is found when querying 3k44 directly.

No hit is found for 3k44 when querying the entire PDB database.

Steps to Reproduce

Run the first command to query against 3k44 directly.

Run the second command to query against the entire PDB database.

Compare the results for 3k44.