Table 2.

Functional annotation tools that can be used in microbial genome annotation

Tool	Description	Source
(Meta)GeneMark	A webpage that provides access to gene prediction in metagenomes	[24]
(Meta)Prodigal	Gene prediction software that is used to identify protein-coding genes in prokaryotic genomes	[29]
MetaGeneAnnotator	Predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths	[47]
CDD	Comprises protein domains conserved throughout molecular evolution	[41]
ChEBI	The CHEBI database contains manually curated data on chemical entities	[26]
GO FEAT	A web-based functional annotation tool for genomic and transcriptomic data	[5]
GO	The Gene Ontology database provides a standardized vocabulary for describing gene function	[2, 9]
KEGG	Links genomic data and higher-order functional information	[32]
Rhea	Rhea is a database that contains functional annotations for enzymes and descriptions of metabolic pathways. The annotations in Rhea are based on expert-curated, non-redundant information on biochemical reactions	[43]
InterPro	InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites	[53]
NCBI Blast	BLAST is a program that identifies regions of similarity between sequences	[30]
SEED	The SEED database provides genome annotations across thousands of genomes	[52]
UniProt	A freely accessible resource on protein sequences and functional annotation	[11]
RefSeq	RefSeq provides a well-annotated set of sequences, including genomic DNA, transcripts, and proteins	[48]
FunMappOne	FunMappOne is a tool for functional analysis and visualization of gene lists	[60]
g:Profiler	Web server for functional enrichment analysis and additional information mining	[37]
GAEV	A tool that was developed for the construction of complete sets of molecular pathways for non-model organisms using KEGG gene function annotations	[73]
GOPlot	GOPlot is an R package for the functional analysis of gene lists	[69]