SEQIN-ST and CODFREG: a full screen sequence editor and a codon usage analysis program for the Atari ST.
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Amino Acid Sequence↗
Biomedical subjects
K Stüber
Publications and source records attributed to K Stüber.
Recognition of ill-defined signals in nucleic acid sequences.
A set of programs has been developed for the definition and handling of nucleic acid sequence consensus information. The sequences of known genetic control signals are combined in a matrix. The origins and positions of the signals are recorded. Old matrices can be updated dynamically: new signals are included and obsolete ones deleted. Matrices of several different types are computed optionally. Several of these matrices can be combined to find possible new signals. The use of matrices allows the exact quantification of signal qualities. The described programs are part of a program library named GENEXPERT. Application examples given are the search for tRNA genes and the search for promoters in the bacteriophage lambda genome.
Algorithms↗
Discrimination of phytochrome dependent light inducible from non-light inducible plant genes. Prediction of a common light-responsive element (LRE) in phytochrome dependent light inducible plant genes.
We aligned 14 5'-leading sequences of small subunit ribulose-1,5-bisphosphate carboxylase (rbcS) genes. A strong consensus sequence ("CCTTATCAT") was located directly upstream of the TATA-box. The occurrence of this motif in other light dependent phytochrome regulated plant genes led to the calculation of two consensus matrices. With these two matrices we are able to distinguish almost all known light induced plant genes which are phytochrome regulated from non-light induced plant genes indicating, that all these genes share a common light-responsive element (LRE). The results obtained by computer analysis are discussed with regard to experimental data.
Base Sequence↗
GENEXPERT, a program system for nucleic acid sequence structural interpretation.
A program system for nucleic acid sequence analysis has been developed. The detection and prediction of secondary structures in nucleic acids have been especially emphasized. The system is able to handle most of the common problems found with nucleic acid sequencing like testing homologies, searching for reading frames and signals etc., but in addition it is able to locate and predict secondary structures. The predicted structures can either be printed on normal line printers or displayed on drawing devices like plotters or video screens. Another special feature is the data base-like handling of consensus sequence matrices by the programs DYCOM and EAGLE. Detailed descriptions of the programs have been published elsewhere (Stüber, 1985, 1986).
Base Sequence↗
Computer analyses on the structure of junction sites between adenovirus DNA and cellular DNA.
In previous work we have cloned and determined the nucleotide sequence of sites of linkage between mammalian cell DNA and foreign (viral) DNA. These investigations have been performed to study details of the mechanism of recombination in mammalian cells. Cloned lines of adenovirus-transformed cells have been used in the analyses because they constituted cell populations in which the foreign DNA had been fixed at certain sites in the cellular genomes. In the present investigation, these nucleotide sequences at sites of linkage have been subjected to computer-aided analyses. A number of sequence motifs have been determined; sequence features common to all junction sites have not been discernible. In some instances, patch homologies have been detected. At several sites of junction, the cellular DNA sequences seem to be transcriptionally active, even in cells that do not carry foreign DNA. Transcriptional activity may be a necessary but perhaps not sufficient precondition for recombination of mammalian DNA sequences with foreign DNA.
Adenoviridae↗
Nucleic acid secondary structure prediction and display.
A set of programs has been developed for the prediction and display of nucleic acid secondary structures. Information from experimental data can be used to restrict or enforce secondary structural elements. The predictions can be displayed either on normal line printers or on graphic devices like plotters or graphic terminals.
Animals↗
Regulated expression of repetitive sequences including the identifier sequence during myotube formation in culture.
We have isolated and characterized a cDNA of 1183 bp, pL6-411, from rat L6 muscle cells. This cDNA contains repetitive sequences - including two inverted copies of the previously described identifier sequence - as shown by sequence analysis. Repetitive sequences from pL6-411 characterize a family of RNAs which is specifically induced during L6 myotube formation. Another part of the pL6-411 sequence, existing at low-copy number per haploid rat genome, hybridized to two RNAs of 5 kb and 2 kb from L6 myoblasts as well as from L6 myotubes. A third pL6-411-related RNA of 150 bases was detected which hybridized with the repetitive sequence but did not hybridize with the low-copy number part of pL6-411. It appears that the 'identifier' sequence in this population of small RNAs is complementary to one of the 'identifier' copies in the pL6-411-related RNA. Finally, we identified on cDNA pL6-411 the recognition site for the TGGCA-binding protein and in both orientations a total of four putative promoters for RNA polymerase III.
Animals↗
Phosphoenolpyruvate-dependent phosphotransferase system. 1H NMR studies on chemically modified HPr proteins.
The low-pK tyrosyl residue present in the heat-stable proteins (HPr) of all Gram-positive bacteria studied until now has been labeled by tetranitromethane in the HPr of Bacillus subtilis and Streptococcus faecalis. The nitrotyrosyl derivatives obtained are fully active in the complementation assay. The labeled tyrosyl residues could be identified as Tyr-37 in both proteins. Reinvestigation of the low-pK tyrosyl residue in HPr of Staphylococcus aureus resulted in the same assignment. In all three proteins an interaction between nitrotyrosine-37 and the active center His-15 could be observed, leading to an increase in the pK of His-15 and a change of its chemical shift parameters. The 1H NMR lines of the complete aromatic spin system of HPr of B. subtilis could be assigned by the nitration studies. Labeling of Arg-17 in HPr of S. aureus and S. faecalis by 1,2-cyclohexanedione in the presence of borate ions causes an almost complete inhibition of its enzymatic activity. In the NMR spectrum the labeling of the arginyl residue influences the resonance lines of His-15: two new resonance lines for the C-2 protons of equal intensity are observed, a fact that could be explained by two different conformations in slow exchange. The pK value of His-15 was not changed by the labeling, excluding Arg-17 as responsible for the low pK of His-15.
Amino Acid Sequence↗
Amino acid sequence of the amphiphilic phosphocarrier protein factor IIILac of the lactose-specific phosphotransferase system of Staphylococcus.
The lactose-specific factor III of the phosphotransferase system of Staphylococcus aureus is an amphiphilic trimeric protein composed of identical subunits. It is hydrophilic in its unphosphorylated state and can be isolated from the cytoplasmic protein fraction. It becomes a constituent of the membrane-bound phosphotransferase complex upon phosphorylation of a single histidyl residue. The sequence of S. aureus factor IIILac was determined and revealed that the subunits consist of 103 residues corresponding to a Mr of 11 367 and of 34 101 for the native trimer: (sequence; see text) According to this sequence and previous work histidine residue 82 located in the C-terminal part of the polypeptide chain is phosphorylated at the N-3 position by phosphoenolpyruvate, enzyme I, and histidine-containing phosphocarrier protein. The N-terminal part of the protein comprising approximately one-third of the chain exhibits in vitro affinity toward membrane-bound enzyme IILac.
Amino Acid Sequence↗
Phosphoenolpyruvate-dependent protein kinase enzyme I of Streptococcus faecalis: purification and properties of the enzyme and characterization of its active center.
Enzyme I, the phosphoenolpyruvate:protein phosphotransferase (EC 2.7.3.9), which is part of the bacterial phosphoenolpyruvate- (PEP) dependent phosphotransferase system, has been purified from Streptococcus faecalis by using a large-scale preparation. Size exclusion chromatography revealed a molecular weight of 140 000. On sodium dodecyl sulfate gels, enzyme I gave one band with a molecular weight of 70 000, indicating that enzyme I consists of two identical subunits. The first 59 amino acids of the amino-terminal part of the protein have been sequenced. It showed some similarities with enzyme I of Salmonella typhimurium. The active center of enzyme I has also been determined. After phosphorylation with [32P]PEP, the enzyme was cleaved by using different proteases. Labeled peptides were isolated by high-performance liquid chromatography on a reversed-phase column. The amino acid composition or amino acid sequence of the peptides has been determined. The largest labeled peptide was obtained with Lys-C protease and had the following sequence: -Ala-Phe-Val-Thr-Asp-Ile-Gly- Gly-Arg-Thr-Ser-His*-Ser-Ala-Ile-Met-Ala-Arg-Ser-Leu-Glu-Ile-Pro-Ala- Ile-Val-Gly-Thr-Lys-. It has previously been shown that the phosphoryl group is bound to the N-3 position of a histidyl residue in phosphorylated enzyme I. The single His in position 12 of the above peptide must therefore carry the phosphoryl group.
Amino Acid Sequence↗
Visualization of nucleic acid sequence structural information.
Several interactive Pascal programs have been written for the analysis and display of structural information in nucleic acid sequences. Layout procedures were developed to display the homology and repeat matrices of a sequence and to predict and display the secondary structure of RNA/DNA molecules free of overlap and to predict and display internal repeats. No special plotting devices are required because the output is adapted to line printers. Sequences from several DNA database systems can be used as input. These programs are part of a general nucleic acid sequence analysis package.
Algorithms↗