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Domain Of Unknown Function
A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs. The DUF designation is tentative, and such families tend to be renamed to a more specific name (or merged to an existing domain) after a function is identified. History The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database. These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively. Characterisation Structural gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domain
In molecular biology, a protein domain is a region of a protein's Peptide, polypeptide chain that is self-stabilizing and that Protein folding, folds independently from the rest. Each domain forms a compact folded Protein tertiary structure, three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or Disulfide bond, disulfide bridges. Domains often form functional units, such as the calcium-binding EF-hand, EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimera (protein), chimeric ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is currently provided through InterPro website. Uses The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a semi-automated method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of protein families has been widely adopted by biologists because of its wide coverage of proteins and sensible naming conventions. It is used by experimental biologists researching specific proteins, by structural biologists to identify new targets for structure determination, by computational biologists to organise sequences and by evolutionary biologis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DUF2992
The ''yjdF'' RNA motif is a conserved RNA structure identified using bioinformatics. Most ''yjdF'' RNAs are located in bacteria classified within the phylum Bacillota. A ''yjdF'' RNA is found in the presumed 5' untranslated region (5' UTR) of the ''yjdF'' gene in ''Bacillus subtilis'', and almost all ''yjdF'' RNAs are found in the 5' UTRs of homologs of this gene. The function of the ''yjdF'' gene is unknown, but the protein that it is predicted to encode is classified by the Pfam Database as DUF2992. The moderately complex secondary structure and nucleotide positions conserved in the ''yjdF'' RNA motif and the fact that it is likely to be present in 5' UTRs led to the hypothesis that ''yjdF'' RNAs function as riboswitches. One ''yjdF'' RNA is found instead in the presumed 5' UTR of genes encoding enzymes involved in the synthesis of nicotinamide adenine dinucleotide (NAD). These RNAs lack a region of the otherwise conserved ''yjdF'' RNA motif and might be non-functional, o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DUF1220
The Olduvai domain, known until 2018 as DUF1220 ( domain of unknown function 1220) and the NBPF repeat, is a protein domain that shows a striking human lineage-specific (HLS) increase in copy number and appears to be involved in human brain evolution. The protein domain has also been linked to several neurogenetic disorders such as schizophrenia (in reduced copies) and increased severity of autism (in increased copies). In 2018, it was named by its discoverers after Olduvai Gorge in Tanzania, one of the most important archaeological sites for early humans, to reflect data indicating its role in human brain size and evolution. Olduvai domains form the core of '' NBPF'' genes, which first appeared in placental mammals and experienced a rapid expansion in monkeys (simians) through duplication to reach over 20 genes in humans. In humans, Olduvai domains are repeated often dozens of times within these genes. The only other gene an Olduvai domain has been found in is mammalian myomeg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SMART (database)
Simple Modular Architecture Research Tool (SMART) is a biological database that is used in the identification and analysis of protein domains within protein sequences. SMART uses profile-hidden Markov models built from multiple sequence alignments to detect protein domains in protein sequences. The most recent release of SMART contains 1,204 domain models. Data from SMART was used in creating the Conserved Domain Database collection and is also distributed as part of the InterPro database. The database is hosted by the European Molecular Biology Laboratory The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 29 member states, two prospect member states, and one associate member state. EMBL was created in ... in Heidelberg. References External links SMART web site Protein structure Protein classification Protein databases {{bioinformatics-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GGDEF Domain
In molecular biology, a GGDEF domain is a protein domain which appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to act as a diguanylate cyclase and synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from '' Caulobacter crescentus'' show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase Adenylate cyclase (EC 4.6.1.1, also commonly known as adenyl cyclase and adenylyl cyclase, abbreviated AC) is an enzyme with systematic name ATP diphosphate-lyase (cyclizing; 3′,5′-cyclic-AMP-forming). It catalyzes the following reac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
EAL Domain
In molecular biology, the EAL domain is a conserved protein domain. It is found in diverse bacterial signalling proteins. It is named EAL after its conserved residues. The EAL domain may function as a diguanylate phosphodiesterase. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s .... References {{InterPro content, IPR001633 Protein domains ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Genomics
Structural genomics seeks to describe the Protein Structure, 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of protein structure prediction, experimental and modeling approaches. The principal difference between structural genomics and protein structure prediction, traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs. Because protein structure is closely linked with protein func ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domains And DUFs In Different Domains Of Life
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metabolic reactions, DNA replication, Cell signaling, responding to stimuli, providing Cytoskeleton, structure to cells and Fibrous protein, organisms, and Intracellular transport, transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the Nucleic acid sequence, nucleotide sequence of their genes, and which usually results in protein folding into a specific Protein structure, 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called pep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteria
Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit the air, soil, water, Hot spring, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the nitrogen fixation, fixation of nitrogen from the Earth's atmosphere, atmosphere. The nutrient cycle includes the decomposition of cadaver, dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, suc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Eukaryote
The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of Outline of life forms, life forms alongside the two groups of prokaryotes: the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but given their generally much larger size, their collective global biomass is much larger than that of prokaryotes. The eukaryotes emerged within the archaeal Kingdom (biology), kingdom Asgard (Archaea), Promethearchaeati and its sole phylum Promethearchaeota. This implies that there are only Two-domain system, two domains of life, Bacteria and Archaea, with eukaryotes incorporated among the Archaea. Eukaryotes first emerged during the Paleoproterozoic, likely as Flagellated cell, flagellated cells. The leading evolutiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Escherichia Coli
''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly found in the lower intestine of warm-blooded organisms. Most ''E. coli'' strains are part of the normal microbiota of the gut, where they constitute about 0.1%, along with other facultative anaerobes. These bacteria are mostly harmless or even beneficial to humans. For example, some strains of ''E. coli'' benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by harmful pathogenic bacteria. These mutually beneficial relationships between ''E. coli'' and humans are a type of mutualistic biological relationship—where both the humans and the ''E. coli'' are benefitting each other. ''E. coli'' is expelled into the environment within fecal matter. The bacterium grows massi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
