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At least 1,189 records · Page 66Linked to original sources
PubMed1984

Human low-molecular-mass kininogen. Amino-acid sequence of the light chain; homology with other protein sequences.

The complete amino acid sequence of the human low-molecular-mass kininogen light chain has been determined. The peptide chain contains 38 amino acid residues. In position 18 the half-cystine residue which forms the disulfide bridge to the heavy chain was found. Alignment of the present sequence with other kininogen light chain sequences indicated that the amino-terminal part of it is species-specific and the carboxy-terminal part is function-specific. Statistically significant internal homologies between various parts of the low-molecular-mass kininogen sequence as well as homologies between parts of the sequences of kininogen and ribonucleases were observed.

Amino Acid Sequence↗
PubMed1984

The amino-acid sequence of copper/zinc superoxide dismutase from swordfish liver. Comparison of copper/zinc superoxide dismutase sequences.

The amino acid sequence of copper/zinc superoxide dismutase from swordfish (Xiphias gladius) liver has been determined by alignment of the tryptic peptides according to the known sequence of bovine erythrocyte copper/zinc superoxide dismutase. This alignment has resulted in the ligands to the copper (His-47, 49, 76 and 94) and the zinc (His-76, 85, 134 and Asp-97) being conserved in all the copper/zinc superoxide dismutases sequenced so far. Also conserved in the sequences are the cysteines forming the intrachain disulphide bridge (Cys-58 and 160) and the essential arginine (Arg-157). Comparison of the amino acid sequence of swordfish liver copper/zinc superoxide dismutase with the bovine, human, horse, yeast and Photobacterium leiognathi indicates that the swordfish enzyme has a high homology with the other eukaryotic enzymes. Low homology is, however, observed with the P. leiognathi enzyme.

Amino Acid Sequence↗
PubMed1979

Comparison of total sequence of a cloned rabbit beta-globin gene and its flanking regions with a homologous mouse sequence.

The nucleotide sequence of a cloned rabbit chromosomal DNA segment of 1620 nucleotides length which contains a beta-globin gene is presented. The coding regions are separated into three blocks by two intervening sequences of 126 and 573 base pairs, respectively. The rabbit sequence was compared with a homologous mouse sequence. The segments flanking the rabbit gene, as well as the coding regions, the 5' noncoding and part of the 3' noncoding messenger RNA sequences are similar to those of the mouse gene; the homologous introns, despite identical location, are distinctly dissimilar except for the junction regions. Homologous introns may be derived from common ancestral introns by large insertions and deletions rather than be multiple point mutations.

Animals↗
PubMed1986

Characterization of Shigella flexneri sequences encoding congo red binding (crb): conservation of multiple crb sequences and role of IS1 in loss of the Crb+ phenotype.

The ability to bind Congo red (Crb+) is associated with virulence of Shigella flexneri and is encoded by a large, 220-kilobase plasmid. We cloned fragments of this plasmid to isolate the sequences encoding Congo red binding, to determine the degree of conservation of these sequences among S. flexneri strains, and to study the molecular basis for loss of the Crb+ phenotype. At least two separate BamHI fragments cloned into plasmid vectors encode Congo red binding in E. coli or S. flexneri. One Crb+ clone, pTKS2, contains a copy of IS1 adjacent to the crb sequences. IS1 appears to be responsible for deletions leading to loss of Congo red binding in this clone. In addition, this clone was found to integrate into the chromosome at relatively high frequency. Integration resulted in loss of the Crb+ phenotype. A second clone, pTKS15, which has only limited homology to pTKS2, also encodes Congo red binding. The Crb+ phenotype of transformants carrying pTKS15 was detected at 37 degrees C but not at 30 degrees C, and thus it resembles Congo red binding in wild-type S. flexneri. HindIII digests of plasmid DNA from 10 different S. flexneri strains were hybridized to both of these Crb+ clones and to an IS1 probe. More than one fragment hybridized to pTKS2 or pTKS15. In general, the sizes of these fragments were the same in S. flexneri strains of different serotypes, indicating conservation of these sequences. Three of five copies of IS1 were also found on the large S. flexneri plasmids. Two of the copies were on fragments of the same size in each strain. Analysis of Crb- derivatives of the 10 strains indicated that, although IS1 may be closely linked to crb sequences on the 220-kilobase plasmid, it is not responsible for the majority of deletions of this plasmid associated with loss of Congo red binding.

Base Sequence↗
PubMed1975

Occurrence of insertion sequence (IS) regions on plasmid deoxyribonucleic acid as direct and inverted nucleotide sequence duplications.

Insertion sequence (IS) regions have been identified previously as a cause of strongly polar mutations in Escherichia coli and several bacteriophages. The present experiments indicate that genetically characterized IS regions occur on bacterial plasmid deoxyribonucleic acid (DNA) as both direct and inverted DNA sequence duplications. The DNA insertion which has been shown previously (Sharp et al., 1973) to control expression of tetracycline resistance in the R6-5 plasmid, and which occurs as directly and inversely repeated DNA sequences adjacent to the region believed to contain the tetracycline resistance gene, has been identified as IS3. A second genetically characterized insertion sequence (IS1) has been identified as a direct DNA duplication occurring at both junctions of the resistance transfer factor and R-determinant components of R6-5 and related plasmids. A model is presented for the reversible dissociation of resistance transfer factor and R-determinant components of co-integrate R plasmids at the sites of DNA sequence homology provided by the repeated IS regions.

Base Sequence↗
PubMed1973

Acquisition of sequences homologous to host DNA by closed circular simian virus 40 DNA. 3. Host sequences.

A preparation of serially passaged simian virus 40 (SV40) DNA, in which at least 66% of the molecules contain covalently linked cellular DNA sequences, was digested to completion with the Hemophilus influenzae restriction endonuclease. Polyacrylamide gel electrophoresis of the digest showed that the majority of the cleavage products migrated as nine classes of fragments, each class defined by a particular molecular weight. These classes of fragments differ in molecular weight from the fragments produced by the action of the same enzyme on plaque-purified virus DNA. Three classes of fragments were present in less than equimolar amounts relative to the original DNA. The remaining six classes of fragments each contain more than one fragment per original DNA molecule. DNA-DNA hybridization analysis (using the filter method) of the isolated cleavage products demonstrated the presence of highly reiterated cell DNA sequences in two of the nine classes of fragments. A third class of fragments hybridized with high efficiency only to serially passaged SV40 DNA; the level of hybridization to plaque-purified virus DNA was low and there was essentially no hybridization with cell DNA immobilized on filters. It is suggested that this class of fragments contains unique host sequences. It was estimated that at least 27% of the sequences in the substituted SV40 DNA molecules studied are host sequences. The majority of these are probably of the nonreiterated type.

Animals↗
PubMed1985

Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3' end of the viral mRNA leader sequence.

cDNA clones that represent various portions of the coronavirus mouse hepatitis virus strain A59 genome RNA have been constructed. cDNAs were synthesized by transcription of genome RNA by using either oligo(dT) or random oligomers of calf thymus DNA as primers. These cDNAs were converted into double-stranded DNA and cloned into pBR322 by standard techniques. The resulting cloned viral DNA fragments were mapped to viral genes by hybridization with Northern blots of intracellular RNA from mouse hepatitis virus strain A59-infected cells. These cDNA clones map in six of the seven viral genes. Clone g344, 1.8 kilobases, is the largest and encompasses gene 5 (which encodes a nonstructural protein) and gene 6 (which encodes the E1 viral glycoprotein) as well as the intergenic regions preceding genes 5, 6, and 7. Sequencing of parts of this cloned DNA show that these three intergenic regions contain a common 11-nucleotide sequence. This sequence shares homology with the 3' end of the viral mRNA leader sequence. Thus, this common intergenic sequence may contain a binding site for a leader RNA that hybridizes to negative-strand viral RNA at the beginning of each gene to prime mRNA synthesis. The different degrees of homology between the leader and its putative binding site may influence the differential rates of transcription of the various viral mRNAs.

Animals↗
PubMed2007

Sequence handling by sequence analysis toolbox v1.0.

The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl inositol-anchored proteins.

Computational Biology↗
PubMed1975

The structure of the mutant dihydrofolate reductase from Streptococcus faecium. Amino acid sequence of peptide CNBr 7 and complete sequence of the protein.

The complete amino acid sequence of the mutant dihydrofolate reductase from Streptococcus faecium var. Durans strain A has been determined by sequence analysis of peptides produced by tryptic, chymotryptic, thermolytic, and mild acid cleavage of the large peptide CNBr 7 and from previously reported studies. The sequence of the S. faecium enzyme is compared to the reported sequence of dihydrofolate reductase from Escherichia coli and the two are shown to contain two domains of substantial homology. One of these domains consists of the NH2-terminal 60 residues and is considered to contribute the dihydrofolate binding site. The second domain probably contains the dinucleotide binding structure. Comparison of the sequences of the dihydrofolate reductases with those of larger dehydrogenases of known structure failed to show any evidence for homology. Considerations of size and predictions of secondary structure also suggest that the second domain in the reductases has no structural similarity to the nucleotide binding site in the larger dehydrogenases. It is concluded that the two reductases are related, although distantly, but that they have evolved from an ancestral protein different from the primitive predecessor of the other oxidoreductases.

Amino Acid Sequence↗
PubMed1999

[Sequencing and analysis of 16S rDNA sequences for P. cocovenenans subsp farinofermentans].

In order to fix the phylogenetic taxonomic position of P. cocovenenans subsp. farinofermentans and describe its relationships with other closed species, seven primers were designed to amplify and sequence the 16S rDNA of 4 strains of it by using a clonal sequencing or direct sequencing method. The 16S rDNA sequence of the 4 strains were aligned with the 16S rDNA sequences of other species in genus Burkholderia, and the polygenetic tree was produced by using a Clustal V and treeview software. The results showed that P. cocovenenans subsp. farinofermentans was in a high homology with Burkholderia gladioli and Burkholderia cocovenenans, and they formed an independent phylogenetic clustal of genus Burkholderia.

DNA, Recombinant↗
PubMed1977

Studies on cytochrome C. XII. Synthesis of the protected undecapeptide (sequence 66-76) and pentadecapeptide (sequence 66-80) of horse heart cytochrome c.

This paper is part of a series on synthesis of suitably protected peptides covering the 66-104 sequence of horse heart cytochrome c. It describes the preparation, by conventional procedures, of a partially protected N alpha-benzyloxycarbonyl-undecapeptide hydrazide corresponding to the sequence from 66 to 76 (Fragment F), which represents a building block for the synthesis of the entire 66-104 sequence. Moreover, the preparation is described of a partially protected pentadecapeptide corresponding to the sequence region 66 to 80, which represents the key peptide for the semisynthesis of the same COOH-terminal sequence utilizing the natural 81-104 N epsilon-trifluoroacetylated CNBr fragment.

Amino Acid Sequence↗
PubMed1978

Nucleotide sequence of DNA template for the 3' ends of SV40 mRNA. II. The sequence of the DNA fragment EcorII-F and a part of EcorII-H.

The nucleotide sequence for two-thirds of restriction endonuclease fragment EcoRII-F and part of RII-H of SV40 DNA is presented. This segment of SV40 DNA is complementary to the sequence near the 3' end of early mRNA. This sequence could be translated in one reading frame to form a large protein. However, in a second translational frame there are four AUG codons followed by 91 sense triplets, followed by a termination codon. These results provide the sequence for the entire 3' untranslated ends of SV40 early and late mRNAs and for the DNA beyond the 3' ends of the mRNAs. The ends of early and late mRNA are transcribed from the opposite strands of the same segment of DNA. At or beyond the 3' ends of both early and late mRNA are sequences whose transcripts would include uridylic acid-rich products.

Base Sequence↗
PubMed1979

The primary sequence of the late region of polyoma virus DNA II. The expression of the late genes and comparison with DNA sequences of SV40 and BKV.

The nucleotide sequence of the late region of the polyoma virus genome has been deduced, which codes for the major capsid protein VP1 and the C-terminal region of the minor proteins VP2 and VP3. The amino acid sequence of VP1 predicted from the nucleotide sequence is in good agreement with the partial N-terminal sequence 1 and amino acid composition of VP1 2,3. When both nucleotide and amono acid sequences are compared with their counterparts in the related viruses, SV40 4,5 and BKV (R. Young, personal communication), extensive homologies are found along the entire regions of the viral genes. Maximum homologies appear to occur in the regions which code for the C-terminal of VP1, on the contrary of the result of heteroduplex analysis 6 with 6 with SV40 and polyoma virus DNAs.

BK Virus↗
PubMed1986

Sequence of two related P-450 mRNAs transcriptionally increased during rat development. An R.dre.1 sequence occupies the complete 3' untranslated region of a liver mRNA.

Polyclonal antibody against a cytochrome P-450 expressed in adult male rats was utilized to screen a lambda gt-11 library. Two cDNAs were isolated and sequenced. The cDNA and deduced protein sequence revealed that these P-450s correspond to previously isolated P-450 PB1 (Waxman D. T., Ko, A., and Walsh, C., (1983) J. Biol. Chem. 258, 11937-11947) and P-450f (Ryan, D. E., Iida, S., Wood, A. W., Thomas, P. E., Lieber, C. S., and Levin, W., (1984) J. Biol. Chem. 259, 1239-1250). Both P-450s contain 490 amino acids and share 75% similarity with each other and 50% similarity with P-450b and P-450e. Southern blot analysis indicates that these enzymes are part of a small P-450 gene subfamily composed of two or three members. An unusual feature of P-450 PB1 is the presence of a rat brain identifier-type repetitive sequence (R.dre.1) that encompasses the complete 3' untranslated region of the mRNA. This sequence is absent from P-450f mRNA. A cDNA from an apparent allelic form of P-450 PB1 mRNA was isolated and sequenced. This cDNA was identical to the other P-450 PB1 cDNA except for a single base substitution in the R.dre.1 repeat and the presence of a repeat (AAATAAA)13 at the 3' end of the mRNA. By use of a 3' specific probe for P-450f mRNA and a probe common to P-450 PB1 and P-450f mRNAs, the mechanism by which these P-450s are elevated during rat development was studied. Both RNAs are virtually absent in newborn rats and become elevated between 1 and 4 weeks after birth. Maximal levels of P-450f mRNA levels continue to increase up to 12 weeks after birth, and 2-fold higher levels of P-450f mRNA are reached in 12-week-old female rats compared with male rats. P-450 PB1 mRNA reached maximal levels at 4 weeks and no sex difference in mRNA level was detected for P-450 PB1. Nuclear run-on transcription assays confirmed that the increase in these mRNAs is due to transcriptional activation.

Aging↗
PubMed1979

Partial amino acid sequence of the glutamate dehydrogenase of human liver and a revision of the sequence of the bovine enzyme.

The glutamate dehydrogenase from a single human liver has been studied. The subunit size was found to be 55,200 +/- 1,500 by sedimentation equilibrium. The partial specific volume is 0.732 as calculated from the amino acid composition. The sequence was determined by isolation of peptides after cyanogen bromide (CNBr) cleavage; the fraction containing the largest peptides was hydrolyzed by trypsin after maleylation. Studies on these peptides accounted for 454 residues of the 505 residues that are presumably present in the protein. For the 51 residues that were not represented in isolated peptides, we have tentatively assumed that the sequence is the same as that of the bovine enzyme. Methionine and arginine residues in these peptides could be placed on the basis of the specificity of cleavage by CNBr or trypsin. In all, 349 residues were placed in sequence, and were aligned by homology with the corresponding peptides of the bovine and chicken enzymes. From the present information, there are 24 known differences in sequence between the human and bovine enzymes and 41 between the human and chicken enzymes. In addition, the human enzyme contains 4 additional residues at the NH2 terminus as compared to the bovine enzyme. In a peptide from the human enzyme, an additional residue, isoleucine 385, was detected by automated Edman degradation. Reinvestigation of the bovine sequence demonstrated that this residue is also present in the bovine enzyme (and presumably in the chicken enzyme also). Residue 384 of the bovine enzyme, previously reported as Glx has now been shown to be glutamine.

Amino Acid Sequence↗
PubMed1983

Nucleotide sequence of Dictyostelium small nuclear RNA Dd8 not homologous to any other sequenced small nuclear RNA.

The cellular slime mold Dictyostelium discoideum, a lower eukaryote, was shown to contain several species of small nuclear RNA (Takeishi, K., and Kaneda, S. (1981) J. Biochem. (Tokyo) 90, 299-308; Wise, J. A., and Weiner, A. M. (1981) J. Biol. Chem. 256, 956-963). One of these RNAs, Dd9 or D2, was sequenced and found to be homologous to mammalian nucleolar U3 RNA. In the present study, the nucleotide sequence of another Dictyostelium small nuclear RNA Dd8 was determined by direct analysis. The sequence is: (formula; see text) Dd8 RNA contains high proportions of A (34%) and U (30%). No modified nucleotide could be detected in the internal region. Computer-assisted analysis of sequence homology indicated that Dd8 RNA is not homologous to any other small nuclear RNA species sequenced so far.

Base Sequence↗
PubMed1983

[Computer bank of amino acid sequences of protein hormones. Comparative analysis of the sequences in pro-opio-melanocortin, proenkephalin and prodynorphin: detection of phorphin--the 4th repeating peptide in prodynorphin].

Using a BESM-6 computer, a computer system for accumulation and comparative analysis of amino acid sequences (AS) of protein-peptide hormones and their precursors (the so-called computer bank of protein hormone AS) was developed. A Fortran-based program designed for construction of correspondence schemes of AS and their local similarity profiles was elaborated. In combination with the previous programs this system allows a rapid inclusion of the newly deciphered sequences into the corresponding homologous groups, thus complementing the correspondence scheme and specifying the evolution profiles. A comparative analysis of AS in proopiomelanocortin (POMC), proenkephalin (PENK) and prodynorphin (PDIN) revealed evolutionary-conservative and variable sites. The conservative sites of AS are active centers of the hormones. The leu-enkephalin analog, phorphin, the fourth repeating peptide of this precursor, was detected in prodynorphin, which, similar to beta-neo-endorphin, dynorphin and rimorphin may possess a biological activity. The similarity of the effector sites of the melanotropin sequence from POMC to the met-enkephalin sequence from PENK and leu-enkephalin sequence from PDIN as well as to gastrin and cholecystokinin was established. This may suggest that the hormone-receptor complexes in target organs of these hormones are also similar.

Amino Acid Sequence↗
PubMed1981

The amino acid sequence of elongation factor Tu of Escherichia coli. The complete sequence.

The complete amino acid sequence of elongation factor Tu of Escherichia coli has been established by sequencing overlapping cyanogen bromide and tryptic peptides. Sequence analysis of peptides was done primarily by solid-phase Edman degradation. Elongation factor Tu is a single chain polypeptide composed of 393 amino acids (Mr = 43,225). Its NH2 terminus is blocked with an acetyl group, as determined by mass spectroscopy, and lysine 56 is partially methylated. The cysteine residues associated with aminoacyl tRNA and guanosine nucleotide binding are located at positions 81 and 137, respectively. Although elongation factor Tu is coded for by two genes, the only site of microheterogeneity found was at the carboxyl terminus (residue 393), which is either glycine or serine. Comparison of the first 140 amino acids of elongation factor Tu and of elongation factor G shows a strong (31%) sequence homology. In addition, secondary structure calculations predict remarkable conformational similarities between the two proteins. The NH2-terminal region of elongation factor Tu appears to be composed of two beta-sheet domains connected by an exposed, alpha-helical bridge, which includes a 14-amino acid segment released by limited treatment with trypsin. Structural features of the aminoacyl-tRNA binding site are discussed in the light of sequence and other chemical and biochemical data.

Amino Acid Sequence↗