• Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. (biomedcentral.com)
  • The Open Protein Structure Annotation Network (TOPSAN) is a wiki designed to collect, share and distribute information about protein three-dimensional structures The site runs on the MindTouch software. (wikipedia.org)
  • As best-hit approaches, especially bidirectional best-hit [ 12 ], have been widely utilized in searching reliable homologous protein sequences, such as orthologs, as well as functional annotation systems [ 13 , 14 , 15 , 16 ], SFannotation can reliably annotate putative proteins. (genominfo.org)
  • Amino acid sequences of predicted proteins and their annotation for 95 organism species. (biosciencedbc.jp)
  • Protein sequences of a total of 95 organism species were obtained from NCBI, JGI and CGP. (biosciencedbc.jp)
  • In recent years, a number of publicly available meta-servers have been developed for protein sequence annotation [ 6 - 8 ], but public access to these servers is often restricted to a limit that ranges from 1 to 10 protein sequences per HTTP request. (biomedcentral.com)
  • While these servers provide the convenience of a whole genome annotation, they do not accept protein sequences as input and, therefore, cannot run analyses on a set of pre-selected proteins from a given genome or a set of un-related proteins from multiple genomes. (biomedcentral.com)
  • In this paper, we describe a new high-throughput, genome-wide analysis tool for deriving enzymatic functions and other annotations for protein sequences. (biomedcentral.com)
  • Tens of thousands of splice isoforms of proteins have been catalogued as predicted sequences from transcripts in humans and other species. (umich.edu)
  • Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. (expasy.org)
  • Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules. (expasy.org)
  • Owing to the generation of vast amounts of sequencing data by using cost-effective, high-throughput sequencing technologies with improved computational approaches, many putative proteins have been discovered after assembly and structural annotation. (genominfo.org)
  • It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. (sdsc.edu)
  • Mauno Vihinen is well-known for his experience and interest in investigating variations and their effects whether they emerge at molecular levels (DNA, RNA protein), in structural context or in the cellular networks and pathways. (lu.se)
  • The Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships connecting protein kinase sequence, structure, function, and disease in a human and machine-readable format. (biorxiv.org)
  • Here we extend the scope of ProKinO as a discovery tool by including new classes and relationships capturing information on kinase ligand binding sites, expression patterns, and functional features, and demonstrate its application in uncovering new knowledge regarding understudied members of the protein kinase family. (biorxiv.org)
  • Specifically, through graph mining and aggregate SPARQL queries, we identify the p21-activated protein kinase 5 (PAK5) as one of the most frequently mutated dark kinase in human cancers with abnormal expression in multiple cancers, including an unappreciated role in acute myeloid leukemia. (biorxiv.org)
  • The updated ontology browser and a web component, ProtVista, which allows interactive mining of kinase sequence annotations in 3D structures and Alphafold models, provide a valuable resource for the signaling community. (biorxiv.org)
  • Glc7p functions in opposition to key spindle assembly checkpoint protein Aurora kinase (Ipl1p). (yeastgenome.org)
  • A Candida albicans gene (CPH1) was cloned that encodes a protein homologous to Saccharomyces cerevisiae Ste12p, a transcription factor that is the target of the pheromone response mitogen-activated protein kinase cascade. (embl-heidelberg.de)
  • TPR-containing proteins include the anaphase promoting complex (APC) subunits cdc16, cdc23 and cdc27, the NADPH oxidase subunit p67 phox, hsp90-binding immunophilins, transcription factors, the PKR protein kinase inhibitor, and peroxisomal and mitochondrial import proteins. (embl.de)
  • We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical 'MitoPathways' spanning seven broad functional categories relevant to mitochondria. (nih.gov)
  • The project will rely on published whole genome assemblies and gene annotations of various qualities. (lu.se)
  • PSAT stands apart from other sequence-based genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. (biomedcentral.com)
  • Based on a secondary structure prediction, we suggestan all-alpha fold for DAPIN, which is also adopted by apoptotic protein domainsof the CARD, death domain and death effector domain type. (embl.de)
  • PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/ . (biomedcentral.com)
  • We developed SFannotation, a simple and fast functional annotation system that rapidly annotates putative proteins against four extant databases, Swiss-Prot, TIGRFAMs, Pfam, and the non-redundant sequence database, by using a best-hit approach with BLASTP and HMMSEARCH. (genominfo.org)
  • MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine. (nih.gov)
  • Enrichment analysis for protein localization showed that mainly intracellular and cell-associated interacting proteins were identified. (degruyter.com)
  • Screening the array with sera and ileal fluid samples from immunized pigs suggested cross-reactivity among homologous proteins and a general activation of immunity. (frontiersin.org)
  • Then, using BLASTP and HMMSEARCH, SFannotation searches homologous proteins and domains in each refined database using a default threshold (≤10 -5 E-value) and selects the highest-scoring homolog to annotate putative proteins as the best-hit approach, such as single best hit and bidirectional best hit [ 12 , 16 ]. (genominfo.org)
  • However a publicly available, high-throughput meta-server is needed to combine the existing annotation tools from their disparate domains in efforts to support genome-scale sequence annotations, whereby a single-user interface can be used to access a variety of computational tools and the results from these tools. (biomedcentral.com)
  • A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. (nih.gov)
  • The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. (embl.de)
  • This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. (nih.gov)
  • An antibody-protein array of putative immunogenic proteins was developed from a combined bioinformatic, experimental, and literature-based prioritization of homologous parasite proteins. (frontiersin.org)
  • Hopefully, predictions and insights from protein bioinformatics will stimulate many experimental validation studies. (umich.edu)
  • The annotation system is searchable and the user can select any annotations to be an experimental factors in analysis whereby it becomes available to analysis plugins and plot-tools. (lu.se)
  • METHODS: We have analysed short- and long-read RNA sequencing data from breast tumours, breast cancer cell lines, and normal tissues to create a comprehensive annotation of ER transcripts and combined it with experimental studies of full-length protein and six alternative isoforms. (lu.se)
  • From the data collected, all of the 11 hypothetical proteins are either involve in translation, cell transportation, cell growth or cell defense mechanism. (usim.edu.my)
  • All of the 11 hypothetical proteins were annotated, with five of them being the most promising proteins for further analysis. (usim.edu.my)
  • Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. (embl.de)
  • The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis, such as the initiation of anaphase and exit from telophase. (embl-heidelberg.de)
  • With the extensive development of protein bioinformatics, the characterization and modeling of isoform features, isoform functions, and isoform-level networks have advanced notably. (umich.edu)
  • Several ER isoforms have been described, but transcript annotation in public databases is incomplete and inconsistent, and functional differences are not well understood. (lu.se)
  • The DAPIN (Domain in Apoptosis and INterferon response) domain is an 80-100- residue domain which is found in the N terminus of diverse vertebrate and vertebrate-specific viral proteins involved in apoptosis, cancer, inflammation, and immune response. (embl.de)
  • We report the discovery of a protein domain, hereafter referred to as DAPIN, indiverse vertebrate and viral proteins that is associated with tumor biology,apoptosis and inflammation. (embl.de)
  • Here we used an affinity-purification mass spectrometry-based (AP-MS) approach to identify novel and particularly intracellular sGAG-interacting proteins in human bone marrow stromal cells (hBMSC). (degruyter.com)
  • In S. cerevisiae, this process involves inhibition of the karyopherin/importin Kap121p (also known as Pse1p), which acts as the specific nuclear import receptor for several proteins, including Glc7p. (yeastgenome.org)
  • A new protein domain was found in several proteins involved in apoptosis,inflammation, cancer and immune responses. (embl.de)
  • Here, we used a genomics/proteomics approach (including immunoblot experiments from pigs infected with T. suis ) to prioritize putative immunogenic excretory/secretory (E/S) proteins conserved across and specific to several gastrointestinal (GI) parasitic nematode species. (frontiersin.org)
  • Putative proteins are typically annotated using a functional annotation system that uses extant databases, but the expansive size of these databases often causes a bottleneck for rapid functional annotation. (genominfo.org)
  • Since large numbers of putative proteins were discovered from a vast amount of sequencing data generated using high-throughput sequencing technologies, including those of the next and third generation, many automated functional annotation systems have contributed greatly to the annotation of them with minimal manual effort [ 2 ]. (genominfo.org)
  • Proteins that activated immunity are potential antigens for immunization and the multi-omics phylum-spanning prioritization database that was created is a valuable resource for identifying target proteins in a wide array of different parasitic nematodes. (frontiersin.org)
  • Multiple-TPR motif proteins would fold into a right-handed super-helical structure with a continuous helical groove suitable for the recognition of target proteins, hence defining a novel mechanism for protein recognition. (embl.de)
  • The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). (nih.gov)
  • Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons. (uky.edu)
  • Here we present applications of the I-TASSER family of algorithms for folding and functional predictions and the IsoFunc, MIsoMine, and Hisonet data resources for isoform-level analyses of network and pathway-based functional predictions and protein-protein interactions. (umich.edu)
  • This function uses a direct annotation scheme to predict KEGG pathway annotations for proteins in the network derived with the PAND algorithm. (rdrr.io)
  • Many of the protein pathway functions overlap with previous findings on genetic markers associated with variability both in isocyanate biomarker levels and asthma susceptibility, which suggests there are overlapping protein pathways that contribute to both isocyanate toxicokinetics and toxicodynamics. (cdc.gov)
  • PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. (nature.com)
  • Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. (umich.edu)
  • Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis , respectively. (frontiersin.org)
  • The major part of his production relates to variations ranging from protein engineering to effects and mechanisms of variations in protein structures, genes and diseases. (lu.se)
  • A cocktail of five recombinant proteins optimized for conserved GI nematode targets was used immunize pigs and test for active antibody responses in both the serum and intestinal ileal fluid of immunized pigs. (frontiersin.org)
  • Glycosaminoglycans (GAGs) are multifunctional polysaccharides of the extracellular matrix (ECM) responsible for ECM hydration and binding of cations and proteins due to their negative charge. (degruyter.com)
  • It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals. (bvsalud.org)
  • Out of 25 patients with infantile nephropathic cystinosis, 12 have two severely truncating mutations, which is consistent with a loss of functional protein, and 13 have missense or in-frame deletions, which would result in disruption of transmembrane domains and loss of protein function. (embl.de)
  • The chemical reactions and pathways resulting in the breakdown of misfolded proteins via a mechanism in which the proteins are transported to the nucleus for ubiquitination, and then targeted to proteasomes for degradation. (yeastgenome.org)
  • Its location within these proteins andpredicted fold suggests that it functions as a protein-protein interactiondomain, possibly uniting different signaling pathways. (embl.de)
  • An accurate annotation of ER isoforms will aid in interpretation of clinical data and inform functional studies to improve our understanding of the ER in health and disease. (lu.se)
  • The RAST server system is particularly popular and can be used to rapidly annotate many microbial proteins against a specially curated subsystem database [ 5 ]. (genominfo.org)
  • Deciphering protein–protein interactions. (crossref.org)
  • The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. (embl.de)
  • The tetratricopeptide repeat (TPR) is a degenerate 34 amino acid sequence identified in a wide variety of proteins, present in tandem arrays of 3-16 motifs, which form scaffolds to mediate protein-protein interactions and often the assembly of multiprotein complexes. (embl.de)
  • NCBI RefSeq accession and version number (protein), e.g. (lu.se)
  • Symbol" is the name of the node this function predicts KEGG annotation for. (rdrr.io)
  • Ratio" is the proportion of neighboring nodes that have the predicted KEGG annotation. (rdrr.io)
  • Affinity tags can reduce merohedral twinning of membrane protein crystals. (lu.se)
  • By identifying many sGAG-specific interacting proteins, our data provide a resource for upcoming studies aimed at molecular mechanisms and understanding of sGAG cellular effects. (degruyter.com)
  • Directly binding to a specific protein and delivering it to a specific cellular location. (yeastgenome.org)
  • CTNS encodes an integral membrane protein, cystinosin, with features of a lysosomal membrane protein. (embl.de)
  • The recently discovered TPR gene family encodes a diverse group of proteins that function in mitosis, transcription, splicing, protein import and neurogenesis. (embl.de)
  • PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome. (biomedcentral.com)
  • This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. (sdsc.edu)
  • and datamining publicly available metagenomic datasets from the human vaginal tract, to identify protein-coding gene clusters in the bacteria that make up the majority of the microbiome of the vagina. (lu.se)
  • Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. (obofoundry.org)
  • A comparison of the proteins encoded in the recently (nearly) completed humangenome to those from the fly and nematode genomes reveals a major increase in thecomplexity of the apoptotic molecular machinery in vertebrates, in terms of both the number of proteins involved and their domain architecture. (embl.de)
  • One of the primary features that were slowing down TOPSAN were the external real-time feeds on protein pages and advanced search options. (topsan.org)
  • The identification of the intracellular sGAG-interacting proteins could help to unravel these functions. (degruyter.com)
  • The interaction of sGAG with α2-macroglobulin receptor-associated protein (LRPAP1), exportin-1 (XPO1), and serine protease HTRA1 (HTRA1) was confirmed in reverse assays. (degruyter.com)
  • Predicted to enable G protein-coupled receptor activity. (jax.org)
  • Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. (uky.edu)
  • These predicted protein networks can inform future research on the mechanism of allergic airway sensitization by isocyanate s and aid in the development of mitigation strategies to better protect worker health. (cdc.gov)
  • The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. (embl-heidelberg.de)
  • Structure predictions suggested that the gene product, cystinosin, is a novel integral lysosomal membrane protein. (embl.de)