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  • peptide
  • One of the members of this gene family, tpr K, codes for a protein that is predicted to have a cleavable signal peptide and be located in the outer membrane of the bacterium. (nih.gov)
  • Motivated by the idea that the cleavage site position and the amino acid composition of the signal peptide are correlated, new features have been included as input to the neural network. (dtu.dk)
  • The accuracy of cleavage site prediction has increased in the range from 6-17 % over the previous version, whereas the signal peptide discrimination improvement mainly is due to the elimination of false positive predictions, as well as the introduction of a new discrimination score for the neural network. (dtu.dk)
  • Thus, previous versions of SignalP retain value for oomycete effector prediction, as the current version, SignalP 4, was unable to reliably predict the signal peptide of the oomycete Crinkler effectors in the test set. (frontiersin.org)
  • The classical endoplasmic reticulum (ER)/Golgi-dependent secretion pathway in eukaryotes is well-defined and involves recognition of an N-terminal signal peptide that is cleaved off as the protein is translocated across the membrane ( Von Heijne, 1990 ). (frontiersin.org)
  • This is because proteins are localised by cell machinery that recognises signal peptide sequences (similar to a postal address) and moves the protein the appropriate location. (wikipedia.org)
  • The signal peptide is often cleaved off after the destination is reached. (wikipedia.org)
  • PSORT uses known signal peptide sequences to analyse and predict what an input sequence is most likely to cause a localisation to. (wikipedia.org)
  • By analysing a signal peptide sequence and visual localisation by GFP expression, strong evidence is obtained for this role. (wikipedia.org)
  • C7orf43 is mostly uncharged, and this neutral charge distribution is conserved in mammals and reptiles, but bony fishes have at least one negative charge cluster C7orf43 is predicted to have no signal peptide in its first 70 amino acid residues. (wikipedia.org)
  • The protein does not contain a peptide signal protein. (wikipedia.org)
  • One notable exception to this is p21 protein, which appears to be ubiquitylated using its N-terminal amine, thus forming a peptide bond with ubiquitin. (wikipedia.org)
  • pathway
  • The twin-arginine translocation (Tat) pathway is one of two general protein transport systems found in the prokaryotic cytoplasmic membrane and is conserved in the thylakoid membrane of plant chloroplasts. (biomedsearch.com)
  • The defining, and highly unusual, property of the Tat pathway is that it transports folded proteins, a task that must be achieved without allowing appreciable ion leakage across the membrane. (biomedsearch.com)
  • The integral membrane TatC protein is the central component of the Tat pathway. (biomedsearch.com)
  • Consistent with a typical predicted salicylic acid (SA)-responsive element and four predicted ABA-responsive elements (ABREs) in the promoter sequence of ZmCHC1 , the expression of ZmCHC1 instead of ZmCHC2 in maize roots is significantly up-regulated by SA or ABA, suggesting that ZmCHC1 gene may be involved in the SA signaling pathway in maize defense responses. (mdpi.com)
  • The CCVs are uncoated in seconds to form uncoated vesicles that fuse with the early endosome (EE) where the cargo is further sorted, either for recycling back to the plasma membrane, or kept in the endocytic pathway to later endosomes, lysosomes and vacuoles for degradation [ 4 , 5 ]. (mdpi.com)
  • The yeast protein RPN11, which interacts with YPL225W, has a homolog in humans that is a metalloprotease component of 26S proteasome that also degrades proteins targeted for destruction by the ubiquitin pathway. (wikipedia.org)
  • A study using FLAG affinity purification mass spectrometry (AP-MS) to profile protein interactions in the Hippo signaling pathway identified C7orf43 as one of the interacting proteins. (wikipedia.org)
  • AMOTL2 is also known to be an inhibitor of Wnt signaling, a pathway with known associations to cancer development, and to be a factor for angiogenesis, a process essential to tumour maintenance and metastasis. (wikipedia.org)
  • subunit
  • Previous work has demonstrated that the alpha subunit of the H, K-ATPase encodes localization information responsible for this pump's apical distribution, whereas the beta subunit carries the signal responsible for the cessation of acid secretion through the retrieval of the pump from the surface to the regulated intracellular compartment. (nih.gov)
  • By analyzing the sorting behaviors of a number of chimeric pumps composed of complementary portions of the H, K-ATPase alpha subunit and the highly homologous Na,K-ATPase alpha subunit, we have identified a portion of the gastric H,K-ATPase, which is sufficient to redirect the normally basolateral Na,K-ATPase to the apical surface in transfected epithelial cells. (nih.gov)
  • AP-1 complex subunit mu-1 is a protein that in humans is encoded by the AP1M1 gene. (wikipedia.org)
  • AP-2 complex subunit mu is a protein that in humans is encoded by the AP2M1 gene. (wikipedia.org)
  • AP-1 complex subunit mu-2 is a protein that in humans is encoded by the AP1M2 gene. (wikipedia.org)
  • recognition
  • The signal recognition particle (SRP)-induced translation arrest and photo-cross-linking demonstrated that SRP recognized the TMD of rTom20-GFP, but with reduced affinity, while the positive charge at the COOH-terminal flanking segment inhibited the translation arrest. (nih.gov)
  • Characteristics of the internalization signal in the Y543 influenza virus hemagglutinin suggest a model for recognition of internalization signals containing tyrosine. (wikipedia.org)
  • The Membrane Occupation and Recognition Nexus is a repeat is found in multiple copies in several proteins including junctophilins. (wikipedia.org)
  • Mitochondrial
  • Whelan, James 2004-10-06 00:00:00 Mitochondrial biogenesis requires a coordinated expression of both the nuclear and the organellar genomes and specific intracellular protein trafficking, processing and assembly machinery. (deepdyve.com)
  • Most mitochondrial proteins are synthesised as precursor proteins containing an N-terminal extension which functions as a targeting signal, which is proteolytically cleaved off after import into mitochondria. (deepdyve.com)
  • We review our present knowledge on components and mechanisms involved in the mitochondrial protein import process in plants. (deepdyve.com)
  • The mitochondrial protein processing in plants is catalysed by the mitochondrial processing peptidase (MPP), which in contrast to other sources, is integrated into the bc1 complex of the respiratory chain. (deepdyve.com)
  • and mechanisms in volv ed in the mitochondrial protein import process in plants. (deepdyve.com)
  • During the first 48 h following imbibition, an ordered increase in the abundance of transcripts encoding mitochondrial proteins was observed. (deepdyve.com)
  • Co-incident with these changes in transcript levels was dynamic and rapid changes in mitochondrial protein content and mitochondrial function. (deepdyve.com)
  • Proteins representing components of the mitochondrial protein import apparatus are strikingly abundant in dry seeds, and a functional import apparatus was shown to operate 2 h after imbibition. (deepdyve.com)
  • In later developmental stages the capacity for matrix organic acid metabolism was evident, accompanied by the appearance of proteins for TCA cycle components, and coordination of electron transport chain assembly through components encoded in both mitochondrial and nuclear genomes. (deepdyve.com)
  • Characterization of the signal that directs Tom20 to the mitochondrial outer membrane. (nih.gov)
  • glycoprotein
  • The best characterized archaeosortase target is the Haloferax volcanii S-layer glycoprotein, an extensively modified protein with O-linked glycosylations, N-linked glycosylations, and a large prenyl-derived lipid modification toward the C-terminus. (wikipedia.org)
  • Measles virus matrix protein specifies apical virus release and glycoprotein sorting in epithelial cells. (wikipedia.org)
  • Lysosomal-associated membrane protein 1 (LAMP-1) also known as lysosome-associated membrane glycoprotein 1 and CD107a (Cluster of Differentiation 107a), is a protein that in humans is encoded by the LAMP1 gene. (wikipedia.org)
  • Lysosomal-associated membrane protein 1 is a glycoprotein from a family of Lysosome-associated membrane glycoproteins. (wikipedia.org)
  • sequence
  • What are the biochemical consequences of the integration of the MPP into an oligomeric protein complex and how are several hundred presequences of precursor proteins with no sequence similarities and no consensus for cleavage, specifically cleaved off by MPP? (deepdyve.com)
  • The names of both families of proteins reflect roles analogous to sortases in Gram-positive bacteria, with which they share no sequence homology. (wikipedia.org)
  • As shown in the alignment, the protein is highly conserved chemically, although the exact sequence varies. (wikipedia.org)
  • Then it analyses the input sequence by applying the stored rules for various sequence features of known protein sorting signals. (wikipedia.org)
  • The second is a multidomain uncharacterized protein conserved in bacteria: COG4642 which contains the MORN repeat region plus the beginning target sequence (1-211). (wikipedia.org)
  • The ATRNL1 protein is approximately half the length of MEGF8, and contains several of the same conserved domains, including the CUB domain and transmembrane sequence. (wikipedia.org)
  • Using SAPS, a Statistical Analysis of Protein Sequence software, amino acid bias was able to be determined. (wikipedia.org)
  • The primary mRNA transcript sequence has 1214 base pairs and its protein product, UPF0368,is composed of 233 amino acids and has a predicted mass of 26,057 Da. (wikipedia.org)
  • internalization
  • Hussein Naim is a Lebanese-Swiss biochemist and molecular virologist, known for his research in cell biology (membrane protein sorting and internalization) and virology (measles, SARS, HIV and Influenza). (wikipedia.org)
  • 269, 3928-3933 Apical and basolateral coated pits of MDCK cells differ in their rates of maturation into coated vesicles, but not in the ability to distinguish between hemagglutinin proteins with different internalization signals. (wikipedia.org)
  • orthologs
  • The other 286 amino acids are less conserved among orthologs (especially distant orthologs) and belong to no known protein family. (wikipedia.org)
  • The Morn repeats are not identical, but follow a general pattern of beginning with a YeG seqeuence, and specifically the subsequent Glycine residues are well conserved even within microbial orthologs which may suggest that the glycine residues may be important and/or involved in some structural function of the protein. (wikipedia.org)
  • The orthologs of the Morn1 protein are listed below obtained by BLAST analysis. (wikipedia.org)
  • A fairly highly conserved protein, MEGF8 has conserved orthologs from P. paniscus to N. vectensis. (wikipedia.org)
  • interactions
  • poly-N-acetyllactosamine groups which are involved in interactions with selectin and other glycan-binding proteins LAMP1 and LAMP2 glycoproteins comprise 50% of all lysosomal membrane proteins, and are thought to be responsible in part for maintaining lysosomal integrity, pH and catabolism. (wikipedia.org)
  • sequences
  • The high similarities of gene structure, protein sequences and 3D models among ZmCHC1 , and Arabidopsis AtCHC1 and AtCHC2 suggest their similar functions in CME. (mdpi.com)
  • We observe that for a set of fungal SwissProt protein sequences, SignalP 4 and the neural network predictors of SignalP 3 ( D -score) and SignalP 2 perform best. (frontiersin.org)
  • genome
  • We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. (biomedcentral.com)
  • A genome that encodes one archaeosortase may encode over fifty target proteins. (wikipedia.org)
  • predict
  • We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). (biomedcentral.com)
  • The aim is to build tools that can accurately predict the outcome of protein targeting in cells. (wikipedia.org)
  • Researchers using this tool can predict with some degree of reason, where in a cell a protein is most likely to localise to. (wikipedia.org)
  • endoplasmic reticulum
  • In yeast, there are at least two vesicle populations upon ER (endoplasmic reticulum) exit, one containing Gap1p (general aminoacid permease) and a glycosylated α-factor, gpαF (glycosylated proα-factor), and the other containing GPI (glycosylphosphatidylinositol)-anchored proteins, Gas1p (glycophospholipid-anchored surface protein) and Yps1p. (biochemj.org)
  • EBP is an integral membrane protein of the endoplasmic reticulum. (antibody-antibodies.com)
  • predictors
  • Particularly, some predictors have been developed that can be used to deal with proteins that may simultaneously exist, or move between, two or more different subcellular locations. (wikipedia.org)
  • Predictors can be specialized for proteins in different organisms. (wikipedia.org)
  • Cell Surface
  • For example, secreted proteins and plasma membrane proteins are easily accessible by drug molecules due to their localization in the extracellular space or on the cell surface. (wikipedia.org)
  • Bacterial cell surface and secreted proteins are also of interest for their potential as vaccine candidates or as diagnostic targets. (wikipedia.org)
  • His research was instrumental towards understanding the intracellular mechanisms of viral and membrane protein sorting in epithelial cells and the cell-surface assembly of several RNA viruses. (wikipedia.org)
  • Targeting
  • We analyzed the mitochondria-targeting signal of rat Tom20 (rTom20) in COS-7 cells, using green fluorescent protein (GFP) as the reporter by systematically introducing deletions or mutations into the TMD or the flanking regions. (nih.gov)
  • We conclude that NH(2)-terminal TMD with a moderate hydrophobicity and a net positive charge in the COOH-terminal flanking region function as the mitochondria-targeting signal of the outer membrane proteins, evading SRP-dependent ER targeting. (nih.gov)
  • The genomic context may not necessarily infer function, but Morn1 has been predicted to contain a second peroxisomal targeting signal using PSORTII at residues 451: RLPPAFKHL, which may suggest interaction with PEX10 (see genomic context above). (wikipedia.org)
  • However, it is predicted to have a vacuolar targeting motif starting at residue 258 in the human protein. (wikipedia.org)
  • enzymology
  • In enzymology, an ubiquitin-protein ligase (EC 6.3.2.19) is an enzyme that catalyzes the chemical reaction ATP + ubiquitin + protein lysine ⇌ {\displaystyle \rightleftharpoons } AMP + diphosphate + protein N-ubiquityllysine The 3 substrates of this enzyme are ATP, ubiquitin, and a lysine residue on a protein, whereas its 3 products are AMP, diphosphate, and protein N-ubiquityllysine. (wikipedia.org)
  • regulates
  • Ubiquitination by E3 ligases regulates diverse areas such as cell trafficking, DNA repair, and signaling and is of profound importance in cell biology. (wikipedia.org)
  • complex
  • TatC then recruits TatA family proteins to form the active translocation complex. (biomedsearch.com)
  • The RING-finger E3 ligases are the largest family and contain ligases such as the anaphase-promoting complex (APC) and the SCF complex (Skp1-Cullin-F-box protein complex). (wikipedia.org)
  • F-box proteins contain an F-box, which binds the rest of the SCF complex, and a substrate binding domain, which gives the E3 its substrate specificity. (wikipedia.org)
  • motif
  • Recent work shows that either of two mutations, knockout of the archaeosortase A (artA) gene or permutation of the motif Pro-Gly-Phe (PGF) to Pro-Phe-Gly, blocks attachment of the lipid moiety as well as blocking removal of the PGF-CTERM protein-sorting domain. (wikipedia.org)
  • Archaeosortases fall into a number of distinct subtypes, each responsible for recognizing sorting signals with a different signature motif. (wikipedia.org)
  • Computational
  • Through the development of new approaches in computer science, coupled with an increased dataset of proteins of known localization, computational tools can now provide fast and accurate localization predictions for many organisms. (wikipedia.org)
  • Human
  • Human FAM158A and its paralogs in other species are part of the uncharacterized protein family UPF0172 family, which is a subset of the JAB1/Mov34/MPN/PAD-1 ubiquitin protease protein family. (wikipedia.org)
  • The graph demonstrates this by plotting each species protein similarity to the human protein vs. the time since the species shared a common ancestor. (wikipedia.org)
  • There are no regions significantly different from other human proteins with regard to composition, regions of polarity, or regions of hydrophobicity. (wikipedia.org)
  • C7orf43 (Chromosome 7 Open reading frame 43) is a protein that in human is encoded by the gene C7orf43. (wikipedia.org)
  • The human protein C7orf43 has an isoelectric point of 8.94. (wikipedia.org)
  • Neither of these proteins is well enough understood to indicate for certain the role of C5orf36 in human cells. (wikipedia.org)
  • Around 70 human F-box proteins have been identified. (wikipedia.org)
  • The Human Protein Atlas. (wikipedia.org)
  • green fluores
  • Expression in Arabidopsis cells of cDNAs encoding each of these KATs fused to green fluorescent protein (GFP) at their C-termini showed that three are targeted to peroxisomes while the fourth is apparently cytosolic. (deepdyve.com)
  • Immunolabeling or tagging (such as with a green fluorescent protein) to view localization using fluorescence microscope are often used. (wikipedia.org)
  • effectors
  • Effector molecules may be the products of either secondary metabolite or protein synthesis, however the majority of effectors identified in fungi and oomycetes are the latter. (frontiersin.org)