• Comparison of the deduced amino acid sequences of the CRPs from chlamydial strains indicated that the small CRP is moderately conserved, with 54% identity between C. psittaci 6BC and Chlamydia trachomatis, and the large CRP is highly conserved, with 71% identity between C. psittaci and C. trachomatis and 85% identity between C. psittaci 6BC and Chlamydia pneumoniae. (asm.org)
  • By applying emotif to all of these alignments, we have generated a database called identify , which contains more than 50,000 sequence motifs with specificities varying from one expected false positive prediction in 10 5 tests to as low as one expected false positive prediction in 10 10 tests. (pnas.org)
  • The C-terminal region of PspA did not possess features conserved among numerous other surface proteins, suggesting that PspA is attached to the cell by a mechanism unique among known surface proteins of gram-positive bacteria. (asm.org)
  • This quick tour provides a brief introduction to InterPro, the EBI's database of protein families, domains and functional sites. (ebi.ac.uk)
  • To decipher the major trends in the evolution of these proteins and make functional predictions for uncharacterized domains, we applied a strategy of sequence database search that includes construction of specialized data sets and iterative subsequence masking. (genetics.org)
  • By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs. (mdpi.com)
  • Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated. (biomedcentral.com)
  • The repeat domain of PspA was found to have significant homology with C-terminal repeat regions of proteins from Streptococcus mutans, Streptococcus downei, Clostridium difficile, and S. pneumoniae. (asm.org)
  • The repeats were found to be homologous to sequences hypothesized to be involved in glucan binding in the GTF-I of S. downei and to sequences within the protein products encoded by gtfB and gtfC of S. mutans. (asm.org)
  • Glycosylphosphatidylinositol (GPI) anchoring is a common posttranslational modification of extracellular eukariotic proteins. (imp.ac.at)
  • A typical RLK contains an extracellular receptor domain to perceive a specific signal, a single-pass transmembrane domain to anchor the protein within the membrane, and a cytoplasmic kinase domain to transduce the signal downstream via autophosphorylation followed by further phosphorylation of specific substrates. (biomedcentral.com)
  • The determination of protein and polypeptide primary structure has always been an important area of research in biochemistry. (taylorfrancis.com)
  • Of all the mass spectrometric techniques in use today for polypeptide structure determinations, fast atom bombardment, or FAB analysis, is employed most often. (taylorfrancis.com)
  • The comparative analysis using a curated database of search queries enabled us to gain insights into the extent of conservation and diversity, as well as the possible virulence-associated roles of glycan-associated proteins in members of the Burkholderia spp. (hindawi.com)
  • emotif also can generate motifs that describe possible subfamilies of a protein superfamily. (pnas.org)
  • Multiple sequence alignment of different reelin domain repeats, derived from homologues, suggests specific functions for individual repeats and high sequence conservation across reelin repeats from different organisms, albeit with few unusual domain architectures. (diva-portal.org)
  • The deduced amino acid sequence of the L protein of MuV showed significant homology with those of six other paramyxoviruses, human parainfluenza type 2 virus, Newcastle disease virus, Sendai virus, measles virus, human parainfluenza type 3 virus, and human respiratory syncytial virus. (nih.gov)
  • The author explores protein sequences (primary structures), both individually and in sets (systems) with the help of probability and information tools. (routledge.com)
  • While determining the primary structures of several E. coli ribosomal proteins, he developed manual micro-methods for isolating peptides using two-dimensional separation on cellulose thin layer plates (instead of using a series of chromatography columns) followed by dansyl-Edman degradation. (wikipedia.org)
  • Peptide maps and recoveries from PVDF-bound standard proteins (4 micrograms each) enzymatically digested with this one-step method are compared with those obtained from the standard PVP-40 method. (nih.gov)
  • In addition, peptide maps and internal sequence data from low-level quantities of unknown proteins enzymatically digested with the improved procedure are presented. (nih.gov)
  • The deduced amino acid sequence of the GBP revealed the presence of a signal peptide of 35 amino acids. (asm.org)
  • The repeated sequences may represent peptide segments that are important to glucan binding and may be distributed among GBPs from other bacterial inhabitants of plaque or the oral cavity. (asm.org)
  • First, we have analyzed the sequence-structure-antigenicity correlations of the third variable (V3) loop of gp120 both as a cyclic 35 amino acid long peptide and in the context of the native gp120. (dtic.mil)
  • This book explores the remarkable information correspondences and probability structures of proteins. (routledge.com)
  • Finally, the remaining unassigned proteins may be compared with known protein folds or structures by using sequence-structure alignment or threading methods ( 10 - 16 ). (pnas.org)
  • We have used emotif to generate sets of motifs from all 7,000 protein alignments in the blocks and prints databases. (pnas.org)
  • We identified bacterial homologues, namely a protein family that includes the Escherichia coli universal stress protein UspA, for the MADS-box transcription regulators previously described only in eukaryotes. (genetics.org)
  • We also show that the FUS6 family of eukaryotic proteins contains a putative DNA-binding domain related to bacterial helix-turn-helix transcription regulators. (genetics.org)
  • By combining these highly specific motifs together in a disjunction, we can potentially describe a protein family with both high specificity and sensitivity. (pnas.org)
  • An improved procedure for enzymatic digestion of polyvinylidene difluoride-bound proteins for internal sequence analysis. (nih.gov)
  • An improved and simplified procedure for enzymatic digestion of proteins bound to polyvinylidene difluoride (PVDF) membranes for obtaining internal protein sequence data is presented. (nih.gov)
  • To date, this improved, one-step procedure has been successfully applied to 52 PVDF-bound unknown proteins (0.7-10 micrograms) of varying molecular weight (19-300 kDa) for which internal sequence data were obtained. (nih.gov)
  • The predicted MuV L protein contained distinct elements thought to be essential for RNA polymerase activity. (nih.gov)
  • On the other hand, protein sequence motifs usually are generated manually in an attempt to maximize the sensitivity while sacrificing specificity, thus giving rise to relatively high frequencies of false predictions ( 17 , 18 ). (pnas.org)
  • Among them, 157 clones showed sequences identical to the predictions in the Arabidopsis sequence resource, TAIR8. (biomedcentral.com)
  • We have applied emotif to two large data sets of aligned proteins of families, the blocks and the prints databases ( 7 , 9 , 20 ). (pnas.org)