lga <hit_FS.TARGET.pdb> -4 -ie -o2 -sia -d:4 -gdc_sc -swap.
The templates discovered with PSI-BLAST and HHblits/HHsearch will almost certainly be homologous to the target. However, since Foldseek is sequence-independent and LGA was run in sequence-independent mode, the second step will potentially discover structurally analogous templates as well as homologues too remote for detection by sequence-based searches.
Template-target alignments from these searches were used to adjust domain boundaries. For example, if the domain parsing programs inStep 2 suggest termination of a domain at residue N , but templates covered the target until residue N+i , then the termination point was moved to N+i if this did not contradict the alignment data for the neighboring domain.