Unable to find exact match 20 bp sequence

[tn-7]

I'm trying to query this: SQSSSSGSPPRRPPPGRRPF in the PDB seqres:

pos_pathogen_0
SQSSSSGSPPRRPPPGRRPF

!grep -B 1 SQSSSSGSPPRRPPPGRRPF ../../bin/mmseq2_db/pdb/pdb_seqres_protein.fasta
results in:

7k7r_C mol:protein length:20 EBNA1 peptide AA386-405
SQSSSSGSPPRRPPPGRRPF
7k7r_F mol:protein length:20 EBNA1 peptide AA386-405
SQSSSSGSPPRRPPPGRRPF

However, if I use, !mmseqs easy-search -c 0.8 $fasta ../../bin/mmseq2_db/pdb/pdb_seqres_protein.fasta
pos_ctrl_result tmp --threads 8 > output.txt nothing results.

[milot-mirdita]

We suppress hits like these likely with our false positive suppression mechanisms. You can try disabling masking and compositional bias correction with --mask 0 --comp-bias-corr 0. That might help with finding these hits. Additionally, you can also disable E-values as this would not really be a homology search anymore with -e inf.