The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. The number of sequences in UniProtKB has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. We continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. In addition, the scientific community continues their contributions of publications and annotations to UniProt entries of their interest. Finally, we describe our new website (https://www.uniprot.org/), designed to enhance our users’ experience and make our data easily accessible to the research community. This interface includes access to AlphaFold structures for more than 85% of all entries as well as improved visualisations for subcellular localisation of proteins.

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and non-coding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains and updates the GO knowledgebase. The GO knowledgebase consists of three components: 1) the Gene Ontology – a computational knowledge structure describing functional characteristics of genes; 2) GO annotations – evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and 3) GO Causal Activity Models (GO-CAMs) – mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised and updated in response to newly published discoveries, and receives extensive QA checks, reviews and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, as well as guidance on how users can best make use of the data we provide. We conclude with future directions for the project.

Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genus Meiothermus with validly published names to reclassify this genus. The results indicate that the species of the genus Meiothermus can be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genus Meiothermus to the species Meithermus ruber, Meiothermus cateniformans, Meiothermus taiwanensis, Meiothermus cerbereus, Meiothermus hypogaeus, Meiothermus luteus, Meiothermus rufus and Meiothermus granaticius, for which it is necessary to emend the genus Meiothermus. The species Meiothermus silvanus, which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the species Meiothermus chliarophilus, Meiothermus timidus, Meiothermus roseus and Meiothermus terrae as species of a novel genus for which we propose the epithet Calidithermus gen. nov. The genus Meiothermus was proposed [1] to reclassify three species included in the genus Thermus that grew at lower temperatures, formed red-or yellow-pigmented colonies and possessed two variants of glycolipid 1 (GL-1). The species of the genus Meiothermus comprise 13 species with validly published names, namely Meithermus ruber [2], Meiothermus chliarophilus [1, 3], Meiothermus silvanus [1, 3], Meiothermus cerbereus [4], Meiothermus taiwanensis [5], Meiothermus timidus [6] Meiothermus rufus [7], Meiothermus cateniformans [8], Meiothermus granaticius [9], Meiothermus hypogaeus [10], Meiothermus terrae [11], Meiothermus roseus [12] and Meiothermus luteus [13]. Most of the type strains of species of the genus Meiothermus are red-pigmented but the type strains of M. chliarophilus, M. timidus, M. terrae and M. roseus form yellow-pigmented colonies. The name M. roseus refers to the colour of a diffusible pink pigment on solid R2A medium, although the colonies are yellow-pigmented.

Rod-shaped cells, 0.5-1.0 µm in width and 1.0-1.5 µm in length. Motile by one polar 28 flagellum. Endospores are not observed. Stain Gram-negative. Colonies are non-29 pigmented. Slightly thermophilic and slightly alkaliphilic. Strictly aerobic. Cytochrome 30 c oxidase and catalase positive. Facultatively mixotrophic. Thiosulfate is oxidized to 31 sulfate with the enhancement of growth. Organic acids, proline and glutamine are used as 32 carbon and energy sources; sugars and polyols are not used for growth. 33 Bacteriochlorophyll a and puf genes are not present. Major respiratory quinone is 34 ubiquinone 10. Major polar lipids are phosphatidylcholine, phosphatidylethanolamine, 35 diphosphatidylglycerol, phosphatidylglycerol and two unidentified aminolipids. Major 36 fatty acids are straight chain saturated and unsaturated fatty acids including hydroxy 37 derivatives. 16S rRNA gene sequence affiliates this genus to family Acetobacteraceae.

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