Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database


A starting alignment was built if other sequences with a known PDB structure were available, by performing a GH19 domain structure-based alignment generated through the mmaker command implemented in ChimeraX. Other seed sequences in the same superfamily were added to this fixed structural alignment by the use of “--add” flag option available in MAFFT. If no other structures were available rather than the reference, a sequence-based alignment with other seeds was created with MAFFT “L-INS-i” strategy, improved by adding information of up to 600 close homologues obtained from a search in Uniprot non-redundant Uniref50 database using a restrictive E-value threshold of 10-20. The obtained alignments were manually cut with respect to the length of the GH19 domain of the reference structure and used to generate the new superfamily-specific profile HMMs.

Metadata Access
Creator Orlando, Marco (University of Milano Bicocca)
Publisher DaRUS
Contributor Pleiss, Jürgen
Publication Year 2020
Funding Reference Bundesministerium für Bildung und Forschung, 031B0571A; Deutsche Forschungsgemeinschaft, EXC2075
Rights CC BY 4.0; info:eu-repo/semantics/openAccess;
OpenAccess true
Contact Pleiss, Jürgen (Universität Stuttgart)
Resource Type Dataset
Format application/octet-stream
Size 113564; 83322; 16272; 18605; 403941; 429406
Version 1.0
Discipline Life Sciences; Medicine