Table 1.

List of databases and algorithms used in GTDB

Database or algorithm	Contents for GTDB	Version
CAZy	Genbank Accession, Uniprot Accession, PDB ID, GT name, EC number, Mechanism, GT Family, Organism, Classification,3D Structure Status	17 April 2019
NCBI Protein	Protein sequences	April 2019
NCBI Nucleotide	Coding region sequences	April 2019
NCBI Gene	Gene symbol, Gene ID	April 2019
NCBI PubMed	Reference	April 2019
NCBI Taxonomy	Taxonomy ID	April 2019
RCSB PDB	Literature, Ligand ID, Ligand name, Resolution, Method	April 2019
UniProt	Gene ontology, KEGG orthology, Reaction, Tissue specificity, Developmental stage, Subcellular location, Protein sequences, Kinetics, PH-opt, Temperature-opt, Enzyme ID, Pfam ID	April 2019
Metacyc	Reaction, Reaction ID, VMAX, KCAT, KM, PH-opt, Temperature-opt	23.2
KEGG	Diseases Involved	1 August 2018
EggNOG	Gene ontology, KEGG orthology	5.0.0
DIAMOND	EC number, pathway ID (Metacyc), enzyme ID (Metacyc)
HMMER	Pfam ID, Pfam name	3.2.1