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... The Two-Hit Method • extension step typically accounts for 90% of BLAST’s execution time • key idea: do extension only when there are two hits on the same diagonal within distance A of each other • to maintain sensitivity, lower T parameter – more single hits found – but only small fraction have as ...
... The Two-Hit Method • extension step typically accounts for 90% of BLAST’s execution time • key idea: do extension only when there are two hits on the same diagonal within distance A of each other • to maintain sensitivity, lower T parameter – more single hits found – but only small fraction have as ...
Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae
... et al., 1997), demonstrate that alanine mutants of the above speci®ed residues produce either reduced activity or inactive enzymes. This strongly indicates that nucleotide binding as well as sulfurylase activity involves residues of these motifs. Additionally, a fourth highly conserved motif can be ...
... et al., 1997), demonstrate that alanine mutants of the above speci®ed residues produce either reduced activity or inactive enzymes. This strongly indicates that nucleotide binding as well as sulfurylase activity involves residues of these motifs. Additionally, a fourth highly conserved motif can be ...
SHORT COMMUNICATION DETERMINATION OF AMINO ACIDS
... Figure 1. Box plot of protein content in fresh and commercial RJ samples. For each group of sample, mean, standard deviation, maximum, and minimum values are shown. CONCLUSION This study can be considered as a first approach to characterize Bulgarian RJ based on its amino acid content. Free and tota ...
... Figure 1. Box plot of protein content in fresh and commercial RJ samples. For each group of sample, mean, standard deviation, maximum, and minimum values are shown. CONCLUSION This study can be considered as a first approach to characterize Bulgarian RJ based on its amino acid content. Free and tota ...
Vanadium-Binding Proteins (Vanabins)
... The cDNA regions corresponding to putative mature vanabins were amplified by PCR using specific primer sets with artificial restriction sites as follows: 12F2, 5'-GGA ATT CGG CCC AGG CTG CAA A-3'; 12R2, 5'-CGT CGA CTC ACA CAC AAT TCA A-3'; 15F2, 5'-GGA ATT CGC TCC GGT GGA TTG C-3'; 15R2, 5'-CGT CGA ...
... The cDNA regions corresponding to putative mature vanabins were amplified by PCR using specific primer sets with artificial restriction sites as follows: 12F2, 5'-GGA ATT CGG CCC AGG CTG CAA A-3'; 12R2, 5'-CGT CGA CTC ACA CAC AAT TCA A-3'; 15F2, 5'-GGA ATT CGC TCC GGT GGA TTG C-3'; 15R2, 5'-CGT CGA ...
Residue 2 residue statistics
... any non-hydrogen atoms within each residue are within 3.5 Å of each other. Statistics are ONLY collected for interactions of residues within the same protein of the viral capsid. All viruses used have icosahedral symmetry. A protein was used to collect statistics if it was a ...
... any non-hydrogen atoms within each residue are within 3.5 Å of each other. Statistics are ONLY collected for interactions of residues within the same protein of the viral capsid. All viruses used have icosahedral symmetry. A protein was used to collect statistics if it was a ...
The KIebsieIIa pneumoniae cytochrome bd
... they require a source of low-potential reductant (between -400 and -500 mV at p H 7) as well as a minimum of 16 moles of ATP per mole of N, fixed (see Hill, 1992). The ability to fix N, is widely distributed amongst obligate anaerobic, facultative anaerobic and obligate aerobic prokaryotes (Young, 1 ...
... they require a source of low-potential reductant (between -400 and -500 mV at p H 7) as well as a minimum of 16 moles of ATP per mole of N, fixed (see Hill, 1992). The ability to fix N, is widely distributed amongst obligate anaerobic, facultative anaerobic and obligate aerobic prokaryotes (Young, 1 ...
Poster
... In this project, a number of putative sEH inhibitors were designed. Work was based on previous drug design efforts as well as on the threedimensional structure of the human enzyme (3). sEH crystal structures exhibit two domains with distinct activities—the C-terminal domain catalyzes the epoxide hyd ...
... In this project, a number of putative sEH inhibitors were designed. Work was based on previous drug design efforts as well as on the threedimensional structure of the human enzyme (3). sEH crystal structures exhibit two domains with distinct activities—the C-terminal domain catalyzes the epoxide hyd ...
Insights into antibody catalysis: Structure of an oxygenation
... specific mutations that may clarify the catalytic mechanism of antibody 28B4 and improve its efficiency and stereoselectivity. For example, mutation of TyrL32 to a phenylalanine or tryptophan should provide insight into the importance of the putative cation-pi interaction. Furthermore, the introduct ...
... specific mutations that may clarify the catalytic mechanism of antibody 28B4 and improve its efficiency and stereoselectivity. For example, mutation of TyrL32 to a phenylalanine or tryptophan should provide insight into the importance of the putative cation-pi interaction. Furthermore, the introduct ...
Complementary DNA Sequence of a Human Cytoplasmic Actin
... muscle tissue. The other two, /3- and y-a&in, are called cytoplasmic actins and are typical of non-muscle tissue (Vandekerckhove & Weber, 19786). In the human genome. there are more than 20 actin genes as estimated by hybridization studies using cloned complementary DNA probes derived from mouse or ...
... muscle tissue. The other two, /3- and y-a&in, are called cytoplasmic actins and are typical of non-muscle tissue (Vandekerckhove & Weber, 19786). In the human genome. there are more than 20 actin genes as estimated by hybridization studies using cloned complementary DNA probes derived from mouse or ...
Applied and Environmental Microbiologyy
... For flow-chamber experiments, the strains were tagged with the green fluorescent protein (GFP). This was accomplished by the insertion of a miniTn7PA1/04/03-gfp-T0T1 transposon cassette into the chromosomes of target strains using the suicide construct pBK-miniTn7-gfp3 (25). Plasmid pBK-miniTn7-gfp3 ...
... For flow-chamber experiments, the strains were tagged with the green fluorescent protein (GFP). This was accomplished by the insertion of a miniTn7PA1/04/03-gfp-T0T1 transposon cassette into the chromosomes of target strains using the suicide construct pBK-miniTn7-gfp3 (25). Plasmid pBK-miniTn7-gfp3 ...
The biosynthesis of peptidoglycan lipid
... in the various biosynthetic pathways. This reaction must also occur after each cycle of polymerization of cell wall components (e.g. of peptidoglycan) and the release of the linked saccharides, because the lipid carrier is in most cases liberated in the pyrophosphate form. However, some exceptions e ...
... in the various biosynthetic pathways. This reaction must also occur after each cycle of polymerization of cell wall components (e.g. of peptidoglycan) and the release of the linked saccharides, because the lipid carrier is in most cases liberated in the pyrophosphate form. However, some exceptions e ...
Biocatalytic degradation of pollutants
... Chemotaxis: a role in biodegradation? Researchers in the field of biodegradation are starting to seriously address the possibility of a role for chemotaxis in the biodegradation of pollutants, as indicated by recent reviews [19,20]. Several reports of chemotaxis by specific biodegradative strains to ...
... Chemotaxis: a role in biodegradation? Researchers in the field of biodegradation are starting to seriously address the possibility of a role for chemotaxis in the biodegradation of pollutants, as indicated by recent reviews [19,20]. Several reports of chemotaxis by specific biodegradative strains to ...
The complete nucleotide sequence of the RNA coding for the
... of the genome coding for the non-structural proteins. To simplify sequence analysis this insert was sub-cloned into two halves (pFA206B and pFA2O6a) as described In methods. Detailed restriction analysis of these clones (see Figure 1) allowed a sequencing strategy to be carried out so that most regi ...
... of the genome coding for the non-structural proteins. To simplify sequence analysis this insert was sub-cloned into two halves (pFA206B and pFA2O6a) as described In methods. Detailed restriction analysis of these clones (see Figure 1) allowed a sequencing strategy to be carried out so that most regi ...
Synthetic biology for engineering acetyl coenzyme a
... enzyme complex, and this was found to be higher than the endogenous mitochondrial PDH complex of yeast. As discussed in the paper, PDH expression has been claimed in an earlier study and here a PDC deletion strain was used as background strain (16). In this study, the authors expressed the PDH subun ...
... enzyme complex, and this was found to be higher than the endogenous mitochondrial PDH complex of yeast. As discussed in the paper, PDH expression has been claimed in an earlier study and here a PDC deletion strain was used as background strain (16). In this study, the authors expressed the PDH subun ...
The initiation phase of protein synthesis in eukaryotes
... Figure 7 The binding of the 4E-BPs to eIF4E is regulated by phosphorylation. The 4E-BPs and eIF4Gs compete for a common binding site on eIF4E. Various stimuli increase the phosphorylation of the 4E-BPs. Hyperphosphorylated 4E-BPs have a relatively low affinity for eIF4E. Conversely, a decrease in 4E ...
... Figure 7 The binding of the 4E-BPs to eIF4E is regulated by phosphorylation. The 4E-BPs and eIF4Gs compete for a common binding site on eIF4E. Various stimuli increase the phosphorylation of the 4E-BPs. Hyperphosphorylated 4E-BPs have a relatively low affinity for eIF4E. Conversely, a decrease in 4E ...
Channel-mediated lactic acid transport: a novel function for
... Most of the known bacterial AQP-type isoforms have been identified in Gram-negative bacteria, whereas most of the GLP-type sequences have been found in Gram-positive ones. This asymmetry might be related to the different structures and diffusion properties of the membranes and cell walls in the two ...
... Most of the known bacterial AQP-type isoforms have been identified in Gram-negative bacteria, whereas most of the GLP-type sequences have been found in Gram-positive ones. This asymmetry might be related to the different structures and diffusion properties of the membranes and cell walls in the two ...
Multiple Sequence Alignment
... – The logarithm of the length of the shortest sequence is used as a scaling factor to increase the GOP with increasing length ...
... – The logarithm of the length of the shortest sequence is used as a scaling factor to increase the GOP with increasing length ...
Thyroid Hormones
... iii. Iodide trapping and oxidation to iodine 1. To produce the functional iodinated hormones the follicle cells must accumulate iodide (anions of iodide) from the blood. Since their intracellular concentration of iodides is over 30x higher than that in blood, iodide trapping depends on active transp ...
... iii. Iodide trapping and oxidation to iodine 1. To produce the functional iodinated hormones the follicle cells must accumulate iodide (anions of iodide) from the blood. Since their intracellular concentration of iodides is over 30x higher than that in blood, iodide trapping depends on active transp ...
Two-hybrid screening
Two-hybrid screening (also known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein–protein interactions (PPIs) and protein–DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively.The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay.