{"title":"Comparison of the structure of archaebacterial ribosomal proteins equivalent to proteins L11 and L1 from Escherichia coli ribosomes.","authors":"C Ramirez, L C Shimmin, P P Dennis, A T Matheson","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The sequences of two ribosomal proteins from two widely divergent species of archaebacteria, Halobacterium cutirubrum and Sulfolobus solfataricus, have been deduced from the structure of their respective genes. These two proteins were found to be equivalent to the L11 and L1 ribosomal proteins of the eubacterium Escherichia coli. Sequence comparison revealed that the archaebacterial L11e (equivalent to E. coli L11) proteins are longer than the eubacterial protein due to a C-terminal extension of about 30 residues. The archaebacterial L11e proteins, like the E. coli L11, are rich in proline residues; most of these are conserved. L11 is the most highly methylated protein in the E. coli ribosome. However, sites of methylation are generally not conserved in the archaebacterial L11e proteins. The region of highest sequence similarity between L11 and the archaebacterial L11e proteins is the N-terminal domain. This domain is believed to interact with release factor 1 during termination of translation. The amino acid sequences of the archaebacterial L1e proteins were compared to the eubacterial E. coli L1 and Bacillus stearothermophilus L1e sequences. The archaebacterial L1e proteins are slightly shorter at both their N- and C-termini. A region of high sequence similarity (7 of 14 residues) occurs near the center of the proteins.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 2","pages":"75-9"},"PeriodicalIF":0.0,"publicationDate":"1991-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13104912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"WOBB.C: a portable software package for defining and searching ambiguous sequence patterns.","authors":"J M Claverie, I Sauvaget","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>WOBB.C is a set of C-written programs designed to build and manipulate ambiguous sequence patterns and to locate them within collections of protein or nucleotide sequences. The search module involves the perceptron algorithm introduced by Stormo et al. (1982) [Nucleic Acids Res 10:2997-3011] in the context of biosequence analysis. The originality of WOBB.C resides in its portability and in a flexible interface, allowing the definition of patterns in three different ways: automatically, from a multi-alignment; interactively, from a character string, or from an explicit text file script.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 2","pages":"119-21"},"PeriodicalIF":0.0,"publicationDate":"1991-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13105016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
H Suzuki, A S Kolaskar, S L Samuel, J Otsuka, A Tsugita
{"title":"A protein secondary structure database (PSS).","authors":"H Suzuki, A S Kolaskar, S L Samuel, J Otsuka, A Tsugita","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A protein secondary structure database (PSS) has been designed to correlate the Protein Sequence Database of the PIR-International with the atomic coordinates and bond connectivities database of the Protein Data Bank in the Brookhaven National Laboratory. The present database includes secondary structures determined by X-ray diffraction analysis, but not predicted structures. The database currently contains data from both the Protein Sequence Database and the Protein Data Bank Database, and will encompass the NMR database in the future. The main characteristics of the database are as follows: (1) the secondary structures, sites, regions and domains of structural interest are displayed together with protein primary structures; and (2) the secondary structure of a desired length of peptide fragment is displayed upon request, as are the peptide fragment(s) that correspond to a defined secondary structure. This database also has software to indicate amino acid pairs having hydrogen bonds and to count the occurrence frequency of each pair as well as the conformational parameters widely used in semi-empirical methods of secondary structure prediction.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 2","pages":"97-104"},"PeriodicalIF":0.0,"publicationDate":"1991-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13104916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G S Baldwin, K L Seet, J Callaghan, G Toncich, B H Toh, R L Moritz, M R Rubira, R Simpson
{"title":"Purification and partial amino acid sequence of human aconitase.","authors":"G S Baldwin, K L Seet, J Callaghan, G Toncich, B H Toh, R L Moritz, M R Rubira, R Simpson","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Aconitase has been purified from membranes prepared from both the human gastric carcinoma cell line Okajima and from porcine gastric mucosa by chromatography on concanavalin A-Sepharose and carboxymethyl-Sepharose, and preparative polyacrylamide gel electrophoresis. Automated Edman degradation of the intact proteins yielded no N-terminal amino acid sequence due, presumably, to N-terminal blockage. Sequence analysis of tryptic peptides derived from S-carboxymethyl porcine and human aconitases established the positions of 95 and 64 amino acid residues, respectively. The amino acid sequence data for porcine aconitase was in perfect agreement with the previously reported cDNA-deduced amino acid sequence [Zheng et al. (1990) J Biol Chem 265:2814-2821]. Comparison of the human amino acid sequence data with the cDNA-deduced amino acid sequence of porcine aconitase indicated that these two proteins have 95% amino acid sequence identity within the sequenced region.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 2","pages":"63-7"},"PeriodicalIF":0.0,"publicationDate":"1991-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13104910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Amino acid sequence of the 14-kDa protein in the photosystem I reaction center complex from Synechococcus elongatus Naegeli.","authors":"N Kotani, I Enami, K Aso, A Tsugita","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>One of the small components (14 kDa) of the photosystem I reaction center complex was isolated from a thermophilic alga, Synechococcus elongatus. The amino acid sequence was determined. The protein consists of 137 amino acid residues, corresponding to the molecular mass of 15,319. Alignment of this sequence with the ferredoxin-binding proteins of photosystem I from other cyanobacteria and higher plants suggests the possible biologically important residues and the residues responsible for thermostability in the sequence.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 2","pages":"81-6"},"PeriodicalIF":0.0,"publicationDate":"1991-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13104913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Analysis of inverted repeats in primary structure of proteins.","authors":"A S Kolaskar, S L Samuel","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A computer program has been developed to locate exact inverted repeating subsequences present anywhere in the given primary structure of proteins or nucleic acids. The output is amenable to protein sequence/nucleic acid query (PSQ/NAQ) packages. Our analysis has shown that there is a large number of proteins which have inverted repeats of more than four amino acid residues in length. However, the number is small when conditions such as the existence of more than 20 inverted repeats in given sequence or the existence of inverted repeats having more than five different types of amino acids are applied.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 2","pages":"105-10"},"PeriodicalIF":0.0,"publicationDate":"1991-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13105014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Sequence homology between a beta-galactosidase and some beta-glucosidases.","authors":"B Henrissat","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A significant sequence homology was found between a thermostable beta-galactosidase from Sulfolobus solfataricus and two beta-glucosidases, respectively, from Caldocellum saccharolyticum and from Agrobacterium sp. These glycosidases appear to form a new protein family, since no homology could be detected with established beta-galactosidase or beta-glucosidase families.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 1","pages":"61-2"},"PeriodicalIF":0.0,"publicationDate":"1991-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13084243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Partial sequences of high-molecular-weight cytochrome c isolated from Desulfovibrio vulgaris Miyazaki.","authors":"C Tasaka, M Ogata, T Yagi, A Tsugita","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A polyhemic high-molecular-weight cytochrome c (hmc) of Mr 67,000 was purified from Desulfovibrio vulgaris Miyazaki. This cytochrome is composed of a single peptide chain. Unlike other c-type cytochromes, hmc deteriorates slowly in atmospheric oxygen. Two peptide fragments of Mr 33,100 (L peptide) and Mr 19,100 (S peptide) were isolated and their N-terminal sequences determined to be PLPGATGEQRADLVEIGVMAKFTNLELPKV (L peptide) and GTLPAVAIPEFVTIGVLK (S peptide). The established sequence of the L peptide is homologous to the N-terminal sequence of cytochrome c3 (Mr 26,000) from D. vulgaris Hildenborough, in spite of discrepancies observed in the molecular size and subunit structure of these cytochromes.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 1","pages":"25-7"},"PeriodicalIF":0.0,"publicationDate":"1991-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12821789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification of regulatory building blocks in Escherichia coli genome.","authors":"T Kunisawa, M Nakamura","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The nucleotide sequences of extragenic regions in the Escherichia coli genome are statistically analyzed. Sequence elements with high occurrence frequencies are identified; these elements are: (1) extragenic palindromic sequences, which are markedly distinguishable from the already identified repetitive extragenic palindromic sequences; (2) promoter sequences of purine biosynthetic genes; and (3) rho-independent terminator sequences. The repetitious occurrence and extensive sequence similarities suggest that these elements share common evolutionary origins. Copies of one sequence element would have become distributed to various positions on the genome during evolution and have been fixed at locations that provide a selective advantage. The extragenic regions of the E. coli genome seem to consist of various regulatory 'building blocks', similar to a protein which consists of modules or domains.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 1","pages":"43-7"},"PeriodicalIF":0.0,"publicationDate":"1991-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13083482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structural classification of endogenous regulatory oligopeptides.","authors":"A A Zamyatnin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Based on the criteria of 50% identity in the amino acid sequence, a new method for grouping endogenous regulatory oligopeptides into structural families is presented. Data from the EROP-Moscow data bank on 579 oligopeptides fitting a preset spectrum of functional activities revealed 73 structural oligopeptide groups, 36 of which were called families.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 1","pages":"53-6"},"PeriodicalIF":0.0,"publicationDate":"1991-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13083484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}