Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary ... Generally, this means that pairwise residue identities between the proteins are 30% and greater. However, in some cases similar ... In practice, when the sequence identity in a sequence sequence alignment is low (i.e. ... The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the structural ...

The other UCK protein is uridine-cytidine kinase 1, which shares about 70% sequence identity with UCK2. While UCK1 is expressed ... The Asp-62 residue is responsible for the catalytic activity in the enzyme active site; the acidic side chain of the Asp-62 ... residue deprotonates the 5'-hydroxyl group on the substrate and activates it to attack the γ-phosphorus of ATP. Structural ... The protein encoded by this gene catalyzes the phosphorylation of uridine and cytidine to uridine monophosphate (UMP) and ...

Note that the sequence identity between two proteins is 29%. Structural Alignment Quaternion Maiti, Rajarshi; Gary H. Van ... In case of identical sequence comparison, SuperPose generates "per-residue" RMSD tables and plots that allow users to identify ... After an initial sequence and secondary structure (in case of low sequence identity) alignment, SuperPose generates a ... different sequence lengths but similar structures or sequences; and (v) largely different sequences but largely similar ...

HIII proteins are more closely related to the H2 group by sequence identity and structural similarity, but have substrate ... All RNases H have an active site centered on a conserved sequence motif composed of aspartate and glutamate residues, often ... However, the yeast B and C subunits have very low sequence identity to their homologs in other organisms, and the corresponding ... The B subunit mediates protein-protein interactions between the H2 complex and PCNA, which localizes H2 to replication foci. ...

These aspects include identity, similarity, and homology. Identity means that the sequences have identical residues at their ... a biological database covering protein domains Phylogenetics Sequence alignment software Structural alignment Thompson JD, ... A technique for protein sequences has been implemented in the software program SAGA (Sequence Alignment by Genetic Algorithm) ... Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures ...

... sequence identity. Thirumananseri Kumarevel solved the crystal structure of the HutP protein in the apo-form, binary complex ( ... HutP is a 16.2 kDa protein consisting of 148 amino acid residues. HutP also exists in five other Bacillus species, including B ... 1. T. S. Kumarevel, H. Mizuno, P. K. R. Kumar, Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and ... HutP (Histidine utilizing Protein) is one of the anti-terminator proteins of Bacillus subtilis, which is responsible for ...

... but sequences falling below a 20% sequence identity can have very different structure. Evolutionarily related proteins have ... Uses of the structural models include protein-protein interaction prediction, protein-protein docking, molecular docking, and ... and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has ... sequence identity but only 2-4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop ...

These proteins are about 400 residues in length and probably span the membrane 12 times. Some members of the BenE family can ... identity to each other and limited sequence similarity to members of the Aromatic Acid:H Symporter (AAHS) family (TC# 2.A.1.15 ... As of early 2016, no crystal structural data is available for members of the BenE family. The generalized transport reaction ... Portal: Biology v t e (Articles with short description, Short description matches Wikidata, Protein families, Solute carrier ...

... sequence identity as well as identical disulfide bonds. Despite the structural homology between these two proteins, ... which add stability to the protein and greatly contribute to its structural conformation. The cysteine residues forming these ... This loss of activity appears to result from the absence of key amino acid residues that produce structural differences that ... used residue-specific modifications to identify positively charged residues that were crucial to the blocking activity of ...

In addition, sequences of distantly related proteins with identity lower than 20% can present different folds. In structural ... structural classification and function prediction by protein inter-residue distance patterns". BMC Genomics. 12 Suppl 4 (S4): ... PISCES server for creating non-redundant lists of proteins: Generates PDB list by sequence identity and structural quality ... such as protein-protein interactions (PPI), protein-peptide interactions, protein-ligand interactions (PLI), and protein-DNA ...

The dramatic increase in genome sequencing technology has caused the number of protein sequences deposited into public ... and protein purification strategies for the enzymes targeted for study. The structure core fulfills the structural biology ... The approach leverages conserved features within a given superfamily such as known chemistry, identity of active site ... functional groups, and composition of specificity-determining residues, motifs, or structures to predict function but relies on ...

... a protein secreted by the stomach mucosa; spasmolytic polypeptide (SP) (TFF2), a protein of about 115 residues that inhibits ... The prediction of structural models for all knottin sequences would open new directions for the analysis of interaction sites ... sequence identity and 1.5 to 4 A backbone deviations although they all share a tightly knotted disulfide core. This important ... Gracy, Jérôme; Chiche, Laurent (2010). "Optimizing structural modeling for a specific protein scaffold: Knottins or inhibitor ...

It is closest in sequence to glycine-N-methyl transferase (GNMT). It also shares many structural properties like the shape of ... PNMT is a protein whose encoding gene is found on chromosome 17 in humans. It consists of 4 exons and is a 30 kDa protein. It ... The residue Glutamine 185 is necessary in binding the catecholamine substrate. The replacement of this residue another reduces ... though it shares less sequence identity. Several features of the structure like this folding lip suggest that PNMT is a recent ...

The ORF6 protein is fairly small at 63 amino acid residues long in SARS-CoV and 61 in SARS-CoV-2. The ORF6 sequence is not well ... Like the genes for other accessory proteins, the ORF6 gene is located near those encoding the structural proteins, at the 5' ... conserved and it has a relatively low sequence identity between the two viruses at about 66%. It has an amphipathic N-terminal ... Studies in SARS-CoV suggest that the ORF6 protein exhibits protein-protein interactions with another viral accessory protein, ...

These proteins share 70% sequence identity in their N-terminal domains, but no sequence similarities have been found in the C- ... P22TSP is a homotrimeric structural protein consisting of 666 amino acids. It is noncovalently bound to the neck of the viral ... A deep cleft is formed by a 60-residue insertion on one side along with three smaller 5-25 residue insertions on the other. ... The initial interest in tailspike proteins was in the study of the effect the mutations on protein folding. Some mutations ...

... conservation of sequence identity and a further 10-23% conservative substitution. The protein is highly acidic (pKa of ~ 3.9) ... This flexible conformation suggests that the protein has few structural domains, however it has been suggested that there may ... The mammalian BSP cDNAs encode for proteins averaging 317 amino acids, which includes the 16-residue preprotein secretory ... Deduced protein sequence and chromosomal localization". J. Biol. Chem. 265 (4): 2347-51. doi:10.1016/S0021-9258(19)39982-X. ...

While hephaestin shares 50% amino acid sequence identity with its serum homologue ceruloplasmin, the hephaestin protein ... In particular, these shared features include cysteine residues involved in disulfide bond formation, histidine residues ... and these studies suggest that many of the structural features important in the enzymatic function of the latter are also ... X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro". DNA Res. 5 (3): 169-76 ...

... structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are ... given the structural alignment between a target and a template sequence, highly accurate models of the target protein sequence ... Roughly speaking, high sequence identity suggests that the sequences in question have a comparatively young most recent common ... Structural alignments, which are usually specific to protein and sometimes RNA sequences, use information about the secondary ...

Multiple sequence alignment List of sequence alignment software Structural Classification of Proteins SuperPose Protein ... the side chain atoms generally are not taken into account because their identities differ between many aligned residues. For ... A recent method for pairwise structural alignment of RNA sequences with low sequence identity has been published and ... The structural alignment also implies a corresponding one-dimensional sequence alignment from which a sequence identity, or the ...

Although chemokine receptors share high amino acid identity in their primary sequences, they typically bind a limited number of ... When the molecule GDP is bound to the G-protein subunit, the G-protein is in an inactive state. Following binding of the ... Arimont A, Sun S, Smit MJ, Leurs R, de Esch IJ, de Graaf C (2017). "Structural Analysis of Chemokine Receptor-Ligand ... Four families of chemokine receptors differ in spacing of cysteine residues near N-terminal of the receptor. Chemokine ...

The three deiodinase enzymes share certain structural features in common although their sequence identity is lower than 50%. ... the selenocysteine insertion sequence (SECIS), be present to bind with SECIS binding protein-2 (SBP-2), which binds with ... The iodotyrosine enzymes work on iodinated single tyrosine residue molecules to scavenge iodine, and do not use as substrates ... June 2019). "Genome sequencing and transcriptome analyses of the Siberian hamster hypothalamus identify mechanisms for seasonal ...

... sequence identity with that of WNK1. The overall fold of the kinase domain of WNK1 resembles those of other protein kinases ... The high level of structural similarity between WNK4 and WNK1 allows us to deduce key structural details of WNK4 based on the ... binding groove is formed by the β3-αA interface of WNK proteins where RFXV peptide ligand interacts directly with residues ... Serine/threonine protein kinase WNK4 also known as WNK lysine deficient protein kinase 4 or WNK4, is an enzyme that in humans ...

The structure of Rtt109 is very similar to that of p300, despite there only being 7% sequence identity between the two proteins ... structural proteins, polyamines, and proteins involved in nuclear import. Acetylation of these proteins can alter their ability ... and GCN5 are mammalian GNATs that share a high degree of homology throughout their sequences. These proteins have a 400-residue ... Those in the MYST family have HAT domains that are about 250 residues in length. Many MYST proteins also contain a cysteine- ...

... despite having little sequence identity (ThiS has 14% identity to ubiquitin), share the same protein fold. These proteins also ... For example, SUMO shares only 18% sequence identity, but they contain the same structural fold. This fold is called "ubiquitin ... rather than a lysine residue, in the protein MyoD and has been observed since in 22 other proteins in multiple species, ... coordinating the cellular localization of proteins, activating and inactivating proteins, and modulating protein-protein ...

Richardson and coworkers designed a 79-residue protein with no sequence homology to a known protein. In the 1990s, the advent ... Individual water molecules can sometimes have a crucial structural role in the core of proteins, and in protein-protein or ... In these cases, the amino acid identity of each rotamer can be ignored and all rotamers belonging to different amino acids can ... The goal of protein design is to find a protein sequence that will fold to a target structure. A protein design algorithm must ...

In SARS-CoV, it is 44 amino acid residues and in SARS-CoV-2 it is 43 residues, with about 85% sequence identity. ORF7b is an ... In SARS-CoV, it has been identified incorporating into virions, suggesting it is a minor viral structural protein. A SARS-CoV-2 ... It is a short, highly hydrophobic transmembrane protein of unknown function. ORF7b protein is a transmembrane protein with a ... The protein is probably expressed from subgenomic RNA through leaky scanning. In SARS-CoV, it is localized to the Golgi ...

... sequence identity to the SARS-CoV protein. A number of possible functions for the ORF7a protein have been described. The ... The ORF7a protein is a transmembrane protein with 121 amino acid residues in SARS-CoV-2 and 122 in SARS-CoV. It is a type I ... "Severe Acute Respiratory Syndrome Coronavirus 7a Accessory Protein Is a Viral Structural Protein". Journal of Virology. 80 (15 ... The protein is not essential for viral replication. Studies in SARS-CoV suggest that the protein forms protein-protein ...

... sequence identity. The full-length ORF8 in SARS-CoV encodes a protein of 122 residues. In many SARS-CoV isolates it is split ... Along with the genes for other accessory proteins, the ORF8 gene is located near those encoding the structural proteins, at the ... The cysteine residue responsible for dimerization of the SARS-CoV-2 protein is not conserved in the SARS-CoV sequence. The ... ORF8 in SARS-CoV-2 encodes a protein of 121 amino acid residues with an N-terminal signal sequence. ORF8 forms a dimer that is ...

... query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein ... Most SUMO-modified proteins contain the tetrapeptide consensus motif Ψ-K-x-D/E where Ψ is a hydrophobic residue, K is the ... Although SUMO has very little sequence identity with ubiquitin (less than 20%) at the amino acid level, it has a nearly ... maltose-binding protein) to increase the protein's solubility. SUMO can later be cleaved from the protein of interest using a ...

The genomes of HzNV-2 and HzNV-1 are very similar, sharing a 93.5% sequence identity. Of the 113 putative genes, the viruses ... 3 structural proteins. Both viruses can replicate in cell cultures, though only HzNV-2 can replicate in an insect host. ... It also contains motif cores for DNA binding sites, catalytic residues, the active sites, and topoisomerase. The best ... "Choristoneura fumiferana Granulovirus p74 protein, a highly conserved baculoviral envelope protein". Journal of Biochemistry ...