Protein sequence evolutionary origin homology. Medical search. Frequent questions

The most common sequence alignment for protein is to look for similarity between different sequences in order to infer function or establish evolutionary relationships. (wikipedia.org)
BLOSUM62 is the matrix built using sequences with less than 62% similarity (sequences with ≥ 62% identity were clustered) - Note: BLOSUM 62 is the default matrix for protein BLAST. (wikipedia.org)
In contrast, analogy is a similarity in structure or function that does not reflect a common evolutionary origin. (wormclassroom.org)
Homologous Superfamily - a group of proteins that share a common evolutionary origin, reflected by similarity in their structure, even if sequence similarity is low. (readthedocs.io)
Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. (genomyx.ch)
However, no clear similarity between Munc13s and protein families generally involved in membrane traffic has been reported, despite the essential nature of Munc13s for neurotransmitter release. (elsevierpure.com)
Including such artifacts can result in similarity between non-homologous sequences. (berkeley.edu)
Related Pfam entries are grouped together into clans, the relationship may be defined by similarity of sequence, structure or profile-HMM. (biocode.ltd)
The evolutionary relationships are based on assumptions about how the embryos develop and the similarity in their molecular structure. (answersingenesis.org)
this is an excerpt (very slightly edited) from the original article Terminologies for Gene & Protein Similarity by Julius H. Jackson. (org.ua)
Homology is a qualitative term that describes a relationship between genes and is based upon the quantitative similarity. (org.ua)
Similarity is a quantitative term that defines the degree of sequence match between two compared sequences. (org.ua)
For example, two aligned genes or segments of sequence that are homologous may have varying degrees of similarity based upon identical base matches in the alignment. (org.ua)
In the first sequence alignment in the following figure, the sequences are obviously identical and therefore exhibit 39 matches out of 39 positions aligned, or 100% similarity. (org.ua)
genes or proteins that display the same activity but lack sufficient similarity to imply common origin. (org.ua)

The highly repetitive sequence content of these regions poses a major barrier to their molecular analysis, and the PAR and centromeres remain unassembled or incompletely assembled on many of highest quality reference genomes, including mouse. (jax.org)
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. (biocode.ltd)
Rather than performing a typical BLAST search, Pfam uses profile hidden Markov models, which give greater weight to matches at conserved sites, allowing better remote homology detection, making them more suitable for annotating genomes of organisms with no well-annotated close relatives. (biocode.ltd)
This protein family is largely expanded in land plant genomes. (frontiersin.org)
Of note, the genes encoding these effectors and immunity proteins are widely distributed in Salmonella genomes, suggesting a relevant role in interbacterial competition and virulence. (frontiersin.org)
Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)

Family - a group of proteins that share a common evolutionary origin reflected by their related functions, sequence homology or similarities in their structure. (readthedocs.io)
Nearly all proteins have structural similarities with other proteins, and in some of these cases, share a common evolutionary origin. (berkeley.edu)

While whole gene duplications and deletions are relatively well-studied, the biology of subexonic ( i.e. , within coding exon sequences), copy number variation remains elusive. (nature.com)
The salivary MUC7 gene provides an opportunity for studying such variation, as it harbors copy number variable subexonic repeat sequences that encode for densely O-glycosylated domains (PTS-repeats) with microbe-binding properties. (nature.com)
The PCR products were purified by using the QIAquick Gel Extraction Kit (QIAGEN) and sequenced by using the ABI Prism BigDye Terminator cycle sequencing kit version 3.1 (Applied Biosystems, Carlsbad, CA, USA) with primers homologous to both ends and internal regions of each gene. (cdc.gov)
Sequences were analyzed by using the Sequencher program version 4.1 (Gene Codes Corp., Inc., Ann Arbor, MI, USA), and aligned by using ClustalW ( www.ebi.ac.uk/clustalw ). (cdc.gov)
Notably, the VP7 gene of the Malaysian G3P[9] strain also shared 90% nt homology with human G3 strains isolated in Malaysia in 2004 and 2007. (cdc.gov)
Similar to the VP7 gene, the VP8 subunit of VP4 of the G3P[9] strains from Malaysia exhibited greatest nucleotide homology (98%) with the rotavirus strain isolated from a raccoon dog (RAC-DG5). (cdc.gov)
Relative levels of gene expression throughout development were determined by quantitative polymerase chain reaction (PCR) analysis and in cases where sufficient specific gene sequence was acquired, ribonucleic acid (RNA) probes were generated to evaluate the spatial expression patterns during the period of organogenesis. (europa.eu)
Through sequence- and structure-based phylogenetics, we classify eukaryotic 7TMICs into two families (Class-A and Class-B), which are the result of a gene duplication predating the split(s) leading to Amorphea (animals, fungi, and allies) and Diaphoretickes (plants and allies). (genomyx.ch)
Liu and Ochman (2007) demonstrate that the evolutionary history of the bac flag involves gene duplication and divergence, and common ancestry with secretory systems. (evcforum.net)
The primary amino acid sequence of a protein is a translated version from its gene sequence which carries important messages and information concealed therein. (springeropen.com)
And, as I have stated before, and as countless ID proponents have insisted every time they are asked about gene duplication as it relates to the origins of new proteins, the ID party line is that this is not a change in information. (uncommondescent.com)
The origin of the eukaryotic N- glycosylation pathway is not unique and less straightforward than previously thought: some basic components likely have proteoarchaeal origins, but the pathway was extensively developed before the eukaryotic diversification through multiple gene duplications, protein co-options, neofunctionalizations and even possible horizontal gene transfers from bacteria. (biomedcentral.com)
In this study, two genes in the genome of Arabidopsis thaliana were found to encode for proteins that demonstrated PPOX activity: one gene is At5g49970 coding for a protein now designated AtPPOX-1, and the other gene is At2g46580 coding for a protein now designated AtPPOX-2. (auburn.edu)
In addition, there is limited information regarding the repertoire of effector proteins encoded within T6SS SPI-6 and T6SS SPI-19 gene clusters in S . Dublin. (frontiersin.org)
Each antibacterial effector gene is located upstream of a gene encoding a hypothetic immunity protein, thus conforming an effector/immunity (E/I) module. (frontiersin.org)
Historically, the gene with the cancer-specific mutation, often in small discrete sequences of DNA, is termed an oncogene. (rroij.com)
Paralogous implies that gene duplication and divergence occurred within the same organism/species and divergence of sequence led to divergence of activity. (org.ua)
Orthologs have homologous origin (common ancestor gene) and homologous activity. (org.ua)
Occasionally the %G+C content may be so vastly different from the average gene in the current host that a conclusion of external origin is nearly inescapable. (org.ua)
This work demonstrates that this I-SceI transgenesis technique, when coupled with an understanding of chromatin accessibility, can be a powerful tool for studying how evolutionary changes in gene regulatory mechanisms contributed to the diversification of body plans in deuterostomes. (stanford.edu)
One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)
By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)

If a genetic programme for specifying cartilage cells arose only once during metazoan evolution, elements of a shared molecular fingerprint will be present in both cephalopods and vertebrates, despite their long independent evolutionary history. (europa.eu)
molecular studies are difficult due to the absence of genome sequence data for any cephalopod. (europa.eu)
These ribosomal sequences was functional for the phylogenetic analysis and molecular taxonomic of any bacteria. (ispub.com)
These proteins include dynein, a molecular motor that can cause flagella to bend, and propel the cell relative to its environment or propel water or mucus relative to the cell. (newworldencyclopedia.org)
Evolutionary relationships of animal phyla are based on DNA and molecular evidence due to the lack of fossil evidence of ancestral species. (answersingenesis.org)
The origin and early evolution of chordates: molecular clocks and the fossil record. (palass.org)
The aim of this review is to provide scientific information for better understanding of the evolutionary biology, molecular epidemiology, pathogenesis, diagnosis, and prevention of Lassa fever in Nigeria and other endemic regions worldwide, which can lead to improved control efforts and reduce morbidity and mortality from recurrent epidemics. (bvsalud.org)

Mucins are highly glycosylated proteins that serve a variety of roles in organisms from lubrication to cell-signaling to defense 7 . (nature.com)
Lamarck proposed the first evolutionary theory where the organisms evolved from simple forms. (intechopen.com)
As a result, the origin of eukaryotes from former organisms is one of the most intriguing questions in biology. (biomedcentral.com)
Obviously we have no record of the origin of life, and little or no evolutionary history of the soft-bodied organisms. (answersingenesis.org)
It is hardly surprising, then, that we have so many gaps in the evolutionary history of life, gaps in such key areas as the origin of the multicellular organisms, the origin of vertebrates, not to mention the origins of most invertebrate groups. (answersingenesis.org)
The origin of multicellular life from a group of colonial organisms is a stretch of the imagination and is not based on any physical evidence. (answersingenesis.org)

On a broader scale, our study highlights variable subexonic repeats as a primary source for modular evolutionary innovation that lead to rapid functional adaptation. (nature.com)
Domain - a distinct functional, structural or sequence unit often found associated with other types of domains. (readthedocs.io)
Such an evolutionary relationship allows structure prediction of the MUN domain and suggests functional similarities between MUN domain-containing proteins and multisubunit tethering complexes such as exocyst, conserved oligomeric Golgi complex, Golgi-associated retrograde protein complex, and Dsl1p. (elsevierpure.com)
Proteins are generally consist of one or more functional regions, commonly known as domains. (biocode.ltd)
Another 30,000 pieces of functional information (over and above proteins) are part of cell architecture. (uncommondescent.com)
The male sterilizing factors are produced by recombination of the mitochondrial genome and consist of unusual genes or open reading frames (ORFs) that usually contain a portion of functional mitochondrial genes and sequences of unknown origin ( Hanson and Bentolila, 2004 ). (frontiersin.org)
These unusual ORFs are maternally inherited, and effectively translated into novel mitochondrial proteins, with the resulting failure to produce functional pollen as the sole observed phenotype ( Chen and Liu, 2014 ). (frontiersin.org)
Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites. (ncbs.res.in)

We have sequenced the cloned DNA and have found no homology between the Na + /glucose co-transporter and either the mammalian facilitated glucose carrier or the bacterial sugar transport proteins. (nature.com)
What we see in the bacterial flagellum is an evolutionary history. (evcforum.net)
Here, a phylogenomic analysis was carried out to examine the validity of rival hypotheses suggesting alternative archaeal or bacterial origins to the eukaryotic N- glycosylation pathway. (biomedcentral.com)
While some effector proteins specifically target bacterial or eukaryotic cells, others can target both types of cells (trans-kingdom effectors). (frontiersin.org)

We have now used comparative sequence and structural analyses to study the structure and evolutionary origin of the MUN domain. (elsevierpure.com)
The Structural Classification of Proteins - extended ( SCOPe ) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst all proteins of known structure, along with resources for analyzing the protein structures and their sequences. (berkeley.edu)
SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
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 biologists tracing the origins of proteins. (biocode.ltd)
Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (ncbs.res.in)
DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12. (openwetware.org)

Following the success of comparative analyses to trace back particular machineries to LECA [ 25 - 32 ], the origin and evolution of the eukaryotic N- glycosylation pathway will be studied here. (biomedcentral.com)
More than half of all eukaryotic proteins are glycoproteins, and 90 % of those are N- glycosylated [ 33 ]. (biomedcentral.com)
The Type VI Secretion System (T6SS) is a multiprotein device that has emerged as an important fitness and virulence factor for many Gram-negative bacteria through the injection of effector proteins into prokaryotic or eukaryotic cells via a contractile mechanism. (frontiersin.org)

BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. (wikipedia.org)
In order to fill in this gap, Henikoff and Henikoff introduced BLOSUM (BLOcks SUbstitution Matrix) matrix which led to marked improvements in alignments and in searches using queries from each of the groups of related proteins. (wikipedia.org)
Scores for each position are obtained frequencies of substitutions in blocks of local alignments of protein sequences. (wikipedia.org)
Each family is represented by multiple sequence alignments and a hidden Markov model (HMMs). (biocode.ltd)
Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a method to reliably calculate the occurrence probabilities of sequence alignments via evolutionary processes on an entire sequence. (biomedcentral.com)
First, for each of all types of local pairwise alignments (PWAs) and some typical types of local multiple sequence alignments (MSAs), we numerically computed the total contribution from all parsimonious indel histories and that from all next-parsimonious histories, and compared them. (biomedcentral.com)
First, it is indels but not substitutions that yield the skeletons (or the gap configurations) of the sequence alignments (reviewed, e.g., in [ 7 ]), which provide essential inputs to most homology-based analyses in computational biology. (biomedcentral.com)
Since the groundbreaking works by Bishop and Thompson [ 13 ] and by Thorne, Kishino and Felsenstein [ 14 ], many studies have been done to develop and apply methods to calculate the probabilities of pairwise alignments (PWAs) and multiple sequence alignments (MSAs) under the probabilistic models aiming to incorporate the effects of indels. (biomedcentral.com)

To understand the possible origin of these G3P[9] viruses, we determined the sequence of the genes encoding the 2 outer capsid proteins, viral protein (VP) 7 and VP4, and analyzed their phylogenetic relationship to other rotaviruses. (cdc.gov)
Phylogenetic analysis was conducted by using MEGA version 4.1 and neighbor-joining method with 1,000 bootstrap replicates ( 10 ).The 4 G3P[9] rotavirus strains all exhibited identical nucleotide and amino acid sequences for the regions of VP7 and VP8 subunit of VP4 analyzed. (cdc.gov)
Phylogenetic relationship of nucleotide sequences of genes encoding the outer capsid proteins VP7 and VP4 from G3P[9] rotavirus strains. (cdc.gov)
Phylogenetic analysis revealed 3 distinct clusters among the VP8 sequences obtained from the P[9] strains ( Figure , panel B). Human and animal P[9] strains from Asia grouped together within a single cluster. (cdc.gov)
My PhD work combined phylogenetic, cytogenetic, and quantitative methods to address the genetic and evolutionary causes of species differences in recombination rate. (jax.org)
In order to understand their evolutionary relationship, phylogenetic analysis of AtPPOX-1 and AtPPOX-2 homologs across the three domains of life suggests that AtPPOX-1 and AtPPOX-2 have independent origins. (auburn.edu)

Mutations that disrupt centromere integrity or reduce homology between X- and Y-linked PARs can lead to chromosome segregation errors and constitute important genetic mechanisms for cancer, cellular senescence, and infertility. (jax.org)
In opinion of De Vries, these mutations give origin to a new species that he named "elementary species" [ 1 ], [ 2 ]. (intechopen.com)
These circumstances make it imperative to develop a stochastic model that enables us to reliably calculate the probability of sequence evolution via mutations including insertions and deletions. (biomedcentral.com)
In a recent study published in the journal npj Vaccines , researchers in China designed, produced, and evaluated the neutralization efficacy of a recombinant coronavirus disease 2019 (COVID-19) vaccine containing four hot-spot substitution mutations based on a prefusion-stabilized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) trimer. (news-medical.net)
The World Health Organization (WHO) has classified the SARS-CoV-2 Alpha, Beta, Gamma, Delta, and Omicron variants as variants of concern because they carry mutations in their spike protein that increase their transmissibility and ability to evade vaccine-induced immunity, as compared to the ancestral Wuhan strain. (news-medical.net)
The present study used the HexaPro (S-6P) S-trimer and an Alum/cytosine phosphoguanine (CpG) 7909 dual adjuvant system to create a modified spike trimer vaccine containing the four spike protein substitution mutations commonly found in the five variants of concern. (news-medical.net)
And though we currently understand some about the origins of cancer, its progressive nature or why, in many cases, somatic mutations arise in the first place, we do recognize the ability of cancer to evolve through a multi-step process with sequential clonal and subclonal selection, following Darwinian iconic evolutionary principles. (rroij.com)

Many C1 domains and C1 domain-containing proteins bind phorbol esters, but many others do not. (embl-heidelberg.de)

Bioinformatics strategies were used to find other homologous genes and proteins, which can also degrade HCH present in various bacteria for controlling of pollution and offer clue to prevent its entry in the food chain. (ispub.com)
Homologous sequences are termed homologs and this term may be applied to both genes and proteins. (org.ua)

Moreover, these proteins' remarkable sequence dissimilarity made it uncertain whether disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF, and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. (genomyx.ch)
Thus, analogous genes or proteins are considered a product of convergent evolution. (org.ua)

High nucleotide homology of 96%-98% was also observed when the P[9] strain from Malaysia was compared with other human P[9] rotavirus strains isolated in Japan, Thailand, and China. (cdc.gov)
Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. (cdc.gov)
Diagnosis of Lassa fever has also advanced from basic serological tests to more sophisticated methods such as quantitative real time polymerase chain reaction (qRT-PCR) and sequencing, which are particularly useful for identifying outbreak strains. (bvsalud.org)

We found weak yet significant sequence similarities between the MUN domain and a set of protein subunits from several related vesicle tethering complexes, such as Sec6 from the exocyst complex and Vps53 from the Golgi-associated retrograde protein complex. (elsevierpure.com)
Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences. (openwetware.org)

For each InterPro entry further information is provided showing, for example, the proteins, structures and pathways matching this entry along with taxonomic distribution. (readthedocs.io)
The comparison of several polyisoprenol-based glycosylation pathways from the three domains of life shows that most of the implicated proteins belong to a limited number of superfamilies. (biomedcentral.com)
The implication is that analogous proteins followed evolutionary pathways from different origins to converge upon the same activity. (org.ua)

1 , 2 As protein tertiary structure is often more conserved, 3 recent advances in ab initio protein folding have made structure-based identification of putative homologs feasible. (genomyx.ch)
4 , 5 , 6 We present a pipeline for the identification and characterization of distant homologs and apply it to 7-transmembrane-domain ion channels (7TMICs), a protein group founded by insect odorant and gustatory receptors. (genomyx.ch)
More generally, this study serves as a methodological proof of principle for the identification of extremely distant protein homologs. (genomyx.ch)
In short: Homologs have common origins but may or may not have common activity. (org.ua)
Thus, orthologs are homologs from duplication that precedes speciation, followed by divergence of sequence but not activity in separate species. (org.ua)

Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. (ncbs.res.in)
Binding of neural cell adhesion molecules (N-CAMs) to the cellular prion protein. (academicinfluence.com)

2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. . (ncbs.res.in)

We present a comprehensive list of 54 C1 domains occurring singly or doubly in 34 different proteins. (embl-heidelberg.de)
The presence of different domains in varying combinations in different proteins gives rise to the diverse repertoire of proteins found in nature. (biocode.ltd)

Species diversity in the structure of zonadhesin, a sperm-specific membrane protein containing multiple cell adhesion molecule-like domains. (embl.de)
A pig sperm protein that binds to the extracellular matrix of the egg in a species-specific manner was recently identified and named zonadhesin (Hardy, D. M., and Garbers, D. L. (1995) J. Biol. (embl.de)
However, for thyriothecial species, phylogenies from DNA sequence data and illustrations of scutella remain have been limited. (ubc.ca)
My multivariate analysis showed that the centroids of morphological characters usually differed significantly between pairs of genetically defined species, indicating evolutionary divergence at the level of morphology. (ubc.ca)
Of the delimited species, nine had been collected ten or more times each and were, based on morphology and sequence analysis, undescribed and restricted to North America. (ubc.ca)
2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species. . (ncbs.res.in)
When speciation follows duplication and one homolog sorts with one species and the other with the other species, subsequent divergence of the duplicated sequence is associated with one or the other species. (org.ua)

Rotavirus double-stranded RNA was extracted by using the QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany), and the genes encoding the VP4 and VP7 proteins were amplified by reverse transcription-PCR (RT-PCR). (cdc.gov)
The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)

Inspired by the work of evo-devo biologists, evo-devo complexity theorists look for processes of evolutionary creativity and developmental constraint in any autopoetic complex systems, at any scale. (evodevouniverse.com)
The Pfam classification of protein families has been widely adopted by biologists because of its wide coverage of proteins and sensible naming conventions. (biocode.ltd)

Total 38 nucleotides and 36 proteins sequences of linA and linB were used for constructing the phylogeny. (ispub.com)
Many proteins exist in the so-called "twilight zone" of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny. (genomyx.ch)
In Chapter 2, I present a comprehensive phylogeny of thyriothecial Dothideomycetes based on 4251 nucelotides for 320 taxa, contributing new nuclear rDNA sequence data for 14 thyriothecial fungi. (ubc.ca)

My research leverages the power of the house mouse model system to address open questions in evolutionary genomics. (jax.org)

Previous sequence and limited structure-based searches identified putatively related proteins, mainly in other animals and plants. (genomyx.ch)
Although AtPPOX-1 and AtPPOX-2 are putatively isoenzymes, very little homology was found in their amino acid sequences. (auburn.edu)

Here we describe cloning of this co-transporter by a method new to membrane proteins. (nature.com)
These findings further unify the mechanism of neurotransmitter release with those of other types of intracellular membrane traffic and, in turn, support a role for tethering complexes in soluble N-ethylmaleimide sensitive factor attachment protein receptor complex assembly. (elsevierpure.com)
Since the flagellar filament is external to the cell membrane, this poses an engineering problem: namely, how can we design the flagellum such that a large number of proteins assemble outside the cell? (evcforum.net)

Agnathans recent and fossil, and the origin of jawed vertebrates. (palass.org)
Agnathans and the origin of jawed vertebrates. (palass.org)

172 Computational analysis and prediction of proteins that undergo domain swapping. (ncbs.res.in)
Computational tools to study RNA-protein complexes. (ncbs.res.in)

Recently, metagenomics a new approach to identify culturable and non culturable bacteria with the help of 16S rDNA sequences isolate total DNA from HCH contaminated soil and amplified 16S rDNA through universal primers and confirmed its total population with denaturing gradient gel electrophoresis and sequencing. (ispub.com)

it is generally believed that all the copies in an organism are identical or nearly identical in nucleotide sequence. (ispub.com)

In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins. (wikipedia.org)
They scanned the BLOCKS database for very conserved regions of protein families (that do not have gaps in the sequence alignment) and then counted the relative frequencies of amino acids and their substitution probabilities. (wikipedia.org)
Sequence alignment is a fundamental research method for modern biology. (wikipedia.org)
Scoring metrics (statistical versus biological): When evaluating a sequence alignment, one would like to know how meaningful it is. (wikipedia.org)
Each Pfam family, often known as a Pfam-A entry, consists of a curated seed alignment containing a small set of representative members of the family, profile hidden Markov models (profile HMMs) built from the seed alignment, and an automatically generated full alignment, which contains all detectable protein sequences belonging to the family. (biocode.ltd)
Previously, we presented a perturbative formulation that facilitates the ab initio calculation of alignment probabilities under a continuous-time Markov model, which describes the stochastic evolution of an entire sequence via indels with quite general rate parameters. (biomedcentral.com)
In the second alignment the aligned sequences contain 28 matches out of 39 possible. (org.ua)

Additionally, although the secretion of IL-1ß from P. gingivalis-infected macrophages was dependent on NLRP3, its adaptor protein ASC, or caspase 1, the cleavage of intracellular pro-IL-1ß to the mature form was found to occur independently of NLRP3, its adaptor protein ASC, or caspase 1. (bvsalud.org)
As a consequence of their unique historical origins, the genetic diversity captured in laboratory mice represents an extremely limited sample of the diversity found in wild mouse populations. (jax.org)
Expression of mouse zonadhesin mRNA is evident only within the testis, and the protein is found exclusively on the apical region of the sperm head. (embl.de)
This crucial function was ascribed to a minimal Munc13 region called the MUN domain, which likely participates in soluble N-ethylmaleimide sensitive factor attachment protein receptor complex (SNARE) assembly and is also found in Ca 2+ -dependent activator protein for secretion. (elsevierpure.com)
The fACCD were found 16.18-82.47 kDa proteins having 149-750 amino acid residues. (springeropen.com)
All proteins were found as homo-dimer except ACCNK13, a homo-tetramer. (springeropen.com)
Evolutionists believe they have found a nearly complete fossil sequence for the evolution of modern whales from a land-based mammal called Pakicetus (52 mya, Fig. 2), but there are many problems (Table 1). (tasc-creationscience.org)

the comparative analysis of mitochondrial DNA sequence strongly supports the cyclostome monophyly. (palass.org)

Analysis of 2179 clonal sequences derived from hypervariable region 1 (HVR1) of the HCV genome in samples obtained from patients with acute (n = 49) and chronic (n = 102) HCV infection showed that intra-host HVR1 diversity was 1.8 times higher in patients with chronic than acute infection. (iospress.com)

PPR proteins represent the most frequent protein class among identified Rfs and they exhibit ideal characteristics to evolve into restorer of fertility when the mechanism of restoration implies a post-transcriptional action. (frontiersin.org)

Together, our findings should motivate caution when interpreting conditional alleles, and suggest the exciting possibility of inter-tissue RNA or protein trafficking in modulation of reproductive biology. (elifesciences.org)

In the majority of cases, Rf genes produce proteins that act directly on the CMS conferring mitochondrial transcripts by binding them specifically and promoting processing events. (frontiersin.org)
In the majority of cases, Rf genes produce proteins that bind specifically to the CMS conferring transcripts in the mitochondria and promote processing events leading to a strong reduction in the production of mitochondrial CMS-inducing proteins (reviewed in Chen and Liu, 2014 ). (frontiersin.org)

This suggests that the mammalian Na + -driven transporter has no evolutionary relationship to the other sugar transporters. (nature.com)
Mammalian von Willebrand factor (VWF), a multifunctional protein involved in maintaining homeostasis. (embl.de)
Mammalian bone morphogenetic protein-binding (BMP-binding) endothelial regulator protein. (embl.de)

Changing a single amino acid in a protein may reduce its ability to carry out this function, or the mutation may even change the function that the protein carries out. (wikipedia.org)

or nucleic acid or in the structure of an organ that reflects a common evolutionary origin. (wormclassroom.org)
The presence of these cellular cartilaginous tissues outside the chordate lineage may indicate a common origin of cartilage as a metazoan tissue type (homology), or alternatively highlights constraints that animals face in the construction of internal cellular endoskeletons (convergence). (europa.eu)
A comparison of their known functions has identified, besides a common role within protein folding, multiple roles for the cyclophilins within pre-mRNA splicing and cellular signalling, and within transcription and cell cycle regulation for the parvulins. (biomedcentral.com)
PPR proteins have in common a canonical P-type 35 amino acid domain repeated in tandem up to 30 times. (frontiersin.org)
Soft parts, such as skin impressions of dinosaurs, and soft-bodied animals like jellyfish are sometimes preserved, and in some localities may be common, but they give us only brief glimpses of evolutionary histories. (answersingenesis.org)
Homology implies that the compared sequences diverged in evolution from a common origin. (org.ua)
In short: Analogs have common activity but not common origin. (org.ua)

Equipped with kinin-releasing cysteine proteases, T. cruzi trypomastigotes were shown previously to invade non-professional phagocytic cells, such as human endothelial cells and murine cardiomyocytes, through the signalling of G protein-coupled bradykinin receptors (B(2) KR). (bvsalud.org)

Throughout the cell's lifetime, this information is transcribed and replicated by cellular mechanisms to produce proteins or to provide instructions for daughter cells during cell division, and the possibility exists that the DNA may be altered during these processes. (wikipedia.org)
Centromeres provide chromosomal points of attachment to the cellular segregation machinery, linking chromosomes to the proteins that pull them to the cell poles during both somatic and germline cell divisions. (jax.org)
Our work reveals 7TMICs as a cryptic superfamily, with origins close to the evolution of cellular life. (genomyx.ch)

The absence of genomic resources renders the search for paralogous cuttlefish genes dependent upon the presence of highly conserved protein motifs within genes of interest, thus we used a degenerate primer strategy to isolate partial coding sequence from the conserved domains specific to these families. (europa.eu)

By combining analysis of 54 C1 domain sequences with information from previously reported solution and crystal structure determinations and site-directed mutagenesis, profiles are derived and used to classify C1 domains. (embl-heidelberg.de)

Taxonomic distribution of proteins containing VWD domain. (embl.de)
The complete taxonomic breakdown of all proteins with VWD domain is also avaliable . (embl.de)
Click on the protein counts, or double click on taxonomic names to display all proteins containing VWD domain in the selected taxonomic class. (embl.de)
Taxonomic distribution of proteins containing C1 domain. (embl-heidelberg.de)

The percentage used was appended to the name, giving BLOSUM80 for example where sequences that were more than 80% identical were clustered. (wikipedia.org)

The peptidyl-prolyl cis / trans isomerase (PPIase) class of proteins is traditionally comprised of three distinct protein families, the cyclophilins (cyclosporin A binding proteins), FKBPs (FK506 binding proteins) and parvulins, that are linked by their shared ability to catalyse the bond preceding a proline residue between its cis and trans forms. (biomedcentral.com)

Some of the transport proteins have been identified-for example, intestinal brush border Na + /glucose and Na + /proline transporters 1,2 and the brain Na + /Cl - /GABA transporter 3 -and progress has been made in locating their active sites and probing their conformational states 1,2,4-7 . (nature.com)
The observed behavior indicates conformational exchange between bound and free states upon protein-micelle interaction. (embl-heidelberg.de)
Fluorescent probes for conformational states of proteins. (academicinfluence.com)

Given the genetic variation," Hagerty explained, "we can't possibly get the original population to below about 10,000 people at any time in our evolutionary history. (salvomag.com)
We can find the stepwise evolutionary history for this system. (evcforum.net)
unpublished data), may indicate a shared early evolutionary history for the cyclophilin and FKBP families. (biomedcentral.com)
Studying the embryonic development of invertebrates reveals their evolutionary history. (answersingenesis.org)
Although the origin and evolutionary history, and the transmission dynamics of Lassa virus have been revealed through recent. (bvsalud.org)

Nevertheless, evolutionary scientists are often quick to assume evolutionary relationships and fill in the gaps of fossil evidence with their imaginations. (tasc-creationscience.org)

Identifying the domains present in a protein can provide insights into the function of that protein. (biocode.ltd)
Editorial: Insights in evolutionary & genomic microbiology: 2022. (openwetware.org)

Built tertiary protein models designated as ACCNK1-ACCNK40 have been deposited in the PMDB with accessions PM0083418-39 and PM0083476-93. (springeropen.com)

Both predicted proteins are highly conserved with other known homologous sequences, with the exception of two small domains present only in the Sof-RXR. (europa.eu)
There are 25698 VWD domains in 12416 proteins in SMART's nrdb database. (embl.de)
There are 58922 C1 domains in 42393 proteins in SMART's nrdb database. (embl-heidelberg.de)
Taxonomy and function of C1 protein kinase C homology domains. (embl-heidelberg.de)
These domains were first discovered as the loci of phorbol ester and diacylglycerol binding to conventional protein kinase C isozymes, which contain 2 C1 domains (C1A and C1B) in their N-terminal regulatory regions. (embl-heidelberg.de)
Proteins containing typical C1 domains are predicted to be regulated by diacylglycerol, whereas those containing only atypical domains are not. (embl-heidelberg.de)
Classical protein kinase C (PKC) family members are activated by the binding of various ligands to one of several cysteine-rich domains of the enzyme. (embl-heidelberg.de)
It provides a complete and accurate classification of protein families and domains. (biocode.ltd)
Pfam has also been used in the creation of other resources such as iPfam, which catalogs domain-domain interactions within and between proteins, based on information in structure databases and mapping of Pfam domains onto these structures. (biocode.ltd)
The PPR protein family is consequently divided in subfamilies depending on the number and type of repeats present in their sequence as well as optional C-terminal domains. (frontiersin.org)

50 amino acids) typically repeated many times within a protein. (readthedocs.io)
The inferred amino acid sequence of AtPPOX-1 is 530 amino acids long and that of AtPPOX-2 is 198 amino acids. (auburn.edu)

The PAR is a region of conserved sequence identity between the X and Y chromosomes over which the meiotic program of pairing, synapsis, and recombination unfolds to ensure correct sex chromosome segregation. (jax.org)

In addition to the main InterPro Entries , which bring together protein signatures from the member databases consortium, InterPro also provides entry pages for the individual member database signatures and for proteins , structures , taxons , proteomes and sets integrated or used by InterPro. (readthedocs.io)
SCOPe undertakes to provide interfaces and data to support all users of protein structure and evolutionary relationships, for research, education, and policy, at scales ranging from interactive exploration of relationships of proteins of interest, including nuances of their individual structures and variations, to comprehensive studies and methods that draw on the entirety of the protein universe. (berkeley.edu)

Given this data, we would hypothesize that: (i) the evolution of the fungal PPIases is driven, at least in part, by the size of the proteome, (ii) evolutionary pressures differ both between the different PPIase families and the different fungi, and (iii) whilst the cyclophilins and parvulins have evolved to perform conserved functions, the FKBPs have evolved to perform more variable roles. (biomedcentral.com)
Then we compared the first-approximate probability of each local MSA with its absolute frequency in the MSAs created via a genuine sequence evolution simulator, Dawg. (biomedcentral.com)
These "evolutionary milestones" occurred at unknown dates and rates, but they must have happened in order for evolution to be true. (answersingenesis.org)
He moved to The USA for graduate training with Greg Wray at SUNY Stonybrook in the Department of Ecology and Evolution, where he worked on the evolution of body plans and the origin of the echinoderms. (stanford.edu)
Following his PhD. he worked as a Miller Fellow at UC Berkeley working on the origin of chordates focussing on the evolution of the vertebrate central nervous system, first in Mike Levine's lab, then with John Gerhart and Marc Kirschner from Harvard. (stanford.edu)

The functionality of a protein is highly dependent on its structure. (wikipedia.org)
Substituting an amino acid with another from the same category is more likely to have a smaller impact on the structure and function of a protein than replacement with an amino acid from a different category. (wikipedia.org)
The present study unveils the structure-function and evolutionary aspects of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) proteins of fungal origin. (springeropen.com)
NMR structure of a protein kinase C-gamma phorbol-binding domain and study of protein-lipid micelle interactions. (embl-heidelberg.de)

The peptidyl-prolyl cis / trans isomerase (PPIase) class of proteins is present in all known eukaryotes, prokaryotes, and archaea, and it is comprised of three member families that share the ability to catalyze the cis / trans isomerisation of a prolyl bond. (biomedcentral.com)
The N- glycosylation is an essential protein modification taking place in the membranes of the endoplasmic reticulum (ER) in eukaryotes and the plasma membranes in archaea. (biomedcentral.com)

Anatomy12

Organisms44

Chemicals and Drugs45

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Psychiatry and Psychology1

Phenomena and Processes96

Disciplines and Occupations4

Anthropology, Education, Sociology and Social Phenomena1

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Information Science29

Health Care6

Similarity15

Genomes6

Share a common evolutionary origin2

Gene22

Molecular7

Organisms6

Functional8

Bacterial4

Structural6

Eukaryotic3

Alignments8

Phylogenetic6

Mutations7

Domain-containi1

Genes and proteins2

Convergent2

Strains4

Similarities2

Pathways3

Homologs5

Molecules2

Annotation1

Different proteins2

Species7

Viral2

Biologists2

Phylogeny3

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Putatively2

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Alignment7

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Biology1

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Identical1

Distinct1

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Insights2

Tertiary1

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Evolution5

Structure4

Eukaryotes2