• Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily. (nih.gov)
  • Thus, the conserved motif at the tip of L6 represents an important piece of two-partner secretion machinery. (nih.gov)
  • This motif is conserved in a predicted loop between two β-barrel strands in more distant relatives of FhaC involved in protein transport across or assembly into the outer membranes of bacteria and organelles, suggesting a conserved function in the molecular mechanism of transport. (nih.gov)
  • To search the potential conserved sequence elements, 30 bp upstream and downstream of the conserved slippery sequence motif from 4,545 predicted slippery sites were extracted and analysed using WebLogo36. (nih.gov)
  • Among the chemoreceptors of these species, Tsr, Tar, and Tcp have a well-conserved carboxy-terminal motif (NWET/SF) that is absent in Trg and Tap. (asm.org)
  • Because this approach does not rely on any previously described transcription factor consensus DNA-binding site information or any other predicted motif or the presence of overrepresented sequences, cis -Decoder analysis affords an unbiased 'evo-centric' view of shared single or multiple sequence homologies between different enhancers. (biomedcentral.com)
  • We have examined the functional effects of substitutions of a conserved aspartic acid residue in the second transmembrane domain (D71A) and of residues in the conserved NPXXY motif in the seventh transmembrane domain (N297A and Y301A). (biochemj.org)
  • Moreover, we show that the functionality of LINC-PINT resides in a highly conserved sequence motif that mediates the interaction with PRC2. (biomedcentral.com)
  • Non-coding sequences important for gene regulation, such as the binding or recognition sites of ribosomes and transcription factors, may be conserved within a genome. (wikipedia.org)
  • DNA sequence comparisons of different co-regulating enhancers suggest that many may rely on different combinations of transcription factors to achieve coordinate gene regulation. (biomedcentral.com)
  • A G----A substitution was found at position 130 of the IVS-I which alters the conserved dinucleotide AG present in the consensus acceptor sequence, thus producing a beta (0)-thalassemia. (biomedsearch.com)
  • Although transcription factor consensus DNA-binding sites are detected within CSBs, searches of 2,086 CSBs (27,996 total bp) curated from 35 mammalian and 99 Drosophila characterized enhancers reveal that well over half of the sequences do not correspond to known DNA-binding sites and, as yet, have no assigned function(s) (this paper). (biomedcentral.com)
  • Sequence analysis of the Arabidopsis thaliana genome has revealed numerous transmembrane receptors predicted to bind proteinacious ligands, emphasizing the importance of identifying peptides with signaling function. (semanticscholar.org)
  • Van de Velde J, Heyndrickx K, Vandepoele K. Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. (ugent.be)
  • Nucleic acid sequences that cause secondary structure in the mRNA of a coding gene may be selected against, as some structures may negatively affect translation, or conserved where the mRNA also acts as a functional non-coding RNA. (wikipedia.org)
  • However, the underlying mechanisms remain poorly understood and it is unknown how the sequences of lncRNA dictate their function. (biomedcentral.com)
  • Since the nature of the sequences and the molecular interactions that confer functionality to lncRNAs remain poorly understood, one of the major challenges is to identify the sequence elements that allow lncRNAs to carry out their activities. (biomedcentral.com)
  • Replacement of the conserved Tyr affects the channel properties, but not the secretion activity, suggesting that this residue stabilizes the loop in the resting conformation of FhaC. (nih.gov)
  • These results and phylogenetic analysis suggested that the medaka neu3a is an evolutionally conserved sialidase with regard to enzymatic properties, whereas neu3b is likely to have originally evolved in medaka. (labome.org)
  • According to Haussler, the researchers were launched on their analysis when initial studies hinted at major regions of conserved DNA sequences. (futurepundit.com)
  • Analysis of 2,086 conserved sequence blocks (CSBs), identified from 135 characterized enhancers, reveals most CSBs consist of shorter overlapping/adjacent elements that are either enhancer type-specific or common to enhancers with divergent regulatory behaviors. (biomedcentral.com)
  • sources of other useful primer sequences from published literature are also indicated. (duke.edu)
  • Alternative domains, which have significantly different secondary structure composition from those based on structurally compact units, were identified based on the alignment footprints of curated protein sequence domain families. (biomedcentral.com)
  • These conflicting sequence based domain boundaries perform slightly better than structure domains in structure similarity searches, and there are interesting cases when structure similarity search performance is markedly improved. (biomedcentral.com)
  • This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. (pubmedcentralcanada.ca)
  • Some domain resources, such as PFAM ( 1 ) and ProDom ( 2 ), rely on the automated methods of multiple sequence alignment while others, such as SMART ( 3 ) and CDD ( 4 ), employ careful manual intervention in constructing the domain models. (pubmedcentralcanada.ca)
  • Different methods have been proposed to produce a multiple sequence alignment. (pubmedcentralcanada.ca)
  • Our findings support a conserved functional co-dependence between LINC-PINT and PRC2 and lead us to propose a new mechanism where the lncRNA regulates the availability of free PRC2 at the proximity of co-regulated genomic loci. (biomedcentral.com)
  • Tissue-specific coordinate gene expression requires multiple inputs that involve dynamic interactions between sequence specific DNA-binding transcription factors and their target DNAs. (biomedcentral.com)
  • see Figure 1 ) that allow for the rapid identification of short 6 to 14 bp DNA sequence elements, called cis -Decoder tags ( c DTs), within enhancer CSBs that are also present in CSBs from other enhancers with either related or divergent functions. (biomedcentral.com)
  • While all of the resources share a common interest in protein family classification using sequence similarity as a key factor to achieve their purposes, the focus of each database is different. (biomedcentral.com)
  • Because of the improvement in performance of structure similarity searches using sequence domain boundaries, we are in the process of implementing their inclusion into the VAST search and MMDB resources in the NCBI Entrez system. (biomedcentral.com)
  • The consensus sequence for the methylation sites is Glu- Glu -X-X-Ala-Ser/Thr ( 18 , 35 , 38 , 50 ). (asm.org)