"An Introduction to Sequence Similarity ("Homology") Searching". In
... MAKING AND USING MULTIPLE SEQUENCE ALIGNMENTS The previous sections of this unit have focused on aligning pairs of sequences, or more generally searching an entire database for high-scoring alignments to a query sequence, which requires many pairwise comparisons. However, if one has several members ...
... MAKING AND USING MULTIPLE SEQUENCE ALIGNMENTS The previous sections of this unit have focused on aligning pairs of sequences, or more generally searching an entire database for high-scoring alignments to a query sequence, which requires many pairwise comparisons. However, if one has several members ...
Evolution and Function of the Plant Cell Wall
... (PF01501; 345 amino acids long) domain (referred to as the GT8 domain throughout this article; for details, see “Materials and Methods”) as the query. This HMMER search, using an E-value cutoff of #1e-2, identified 378 nonidentical GT8 domains in 378 proteins from the 15 genomes, which are herein ref ...
... (PF01501; 345 amino acids long) domain (referred to as the GT8 domain throughout this article; for details, see “Materials and Methods”) as the query. This HMMER search, using an E-value cutoff of #1e-2, identified 378 nonidentical GT8 domains in 378 proteins from the 15 genomes, which are herein ref ...
Coordination of the maize transcriptome by a conserved circadian
... with "cellular amino acid and derivative metabolic process" (GO: 0006519), which showed overrepresentation of genes with peak levels at ZT20 (Table 1, Figure 2). These results indicate maize protein synthesis may also have a pre-dawn phase. Interestingly, Arabidopsis genes associated with protein sy ...
... with "cellular amino acid and derivative metabolic process" (GO: 0006519), which showed overrepresentation of genes with peak levels at ZT20 (Table 1, Figure 2). These results indicate maize protein synthesis may also have a pre-dawn phase. Interestingly, Arabidopsis genes associated with protein sy ...
Cloning and Functional Characterization of a Phospholipid
... 97: 6487–6492). The LRO1 gene that encodes the PDAT was identified in yeast (Saccharomyces cerevisiae) and shown to have homology with animal lecithin:cholesterol acyltransferase. A search of the Arabidopsis genome database identified the protein encoded by the At5g13640 gene as the closest homolog ...
... 97: 6487–6492). The LRO1 gene that encodes the PDAT was identified in yeast (Saccharomyces cerevisiae) and shown to have homology with animal lecithin:cholesterol acyltransferase. A search of the Arabidopsis genome database identified the protein encoded by the At5g13640 gene as the closest homolog ...
Deorphanization of GPRC6A: a promiscuous L-α
... variant forms, verified by the exon-intron organization of the gene for hGPRC6A, mapping to chromosome 6q22.31 (Genbank accession #AY435125, AY435126, and AY435127). RT-PCR analysis showed that the longest isoform of GPRC6A was expressed at the highest level in human tissues, and an orthologue of th ...
... variant forms, verified by the exon-intron organization of the gene for hGPRC6A, mapping to chromosome 6q22.31 (Genbank accession #AY435125, AY435126, and AY435127). RT-PCR analysis showed that the longest isoform of GPRC6A was expressed at the highest level in human tissues, and an orthologue of th ...
Drosophila - The Solomon H Snyder Department of Neuroscience
... segments might be rearranged by a particular insertion such as an FRT site; 4) which gene might be overexpressed by an inserted regulatory element; or 5) the location of a transgene for recombination with other genetic elements, such as a mutation or other transgenes. Since transposon integrated tra ...
... segments might be rearranged by a particular insertion such as an FRT site; 4) which gene might be overexpressed by an inserted regulatory element; or 5) the location of a transgene for recombination with other genetic elements, such as a mutation or other transgenes. Since transposon integrated tra ...
Molecular Characterization of NADH-Dependent
... used as a hybridization probe to screen a third cDNA library that had been prepared using a reverse transcriptase lacking RNase H activity. This screening produced numerous hybridizing recombinant phage that contained inserts longer than those previously obtained, including one which was of a size t ...
... used as a hybridization probe to screen a third cDNA library that had been prepared using a reverse transcriptase lacking RNase H activity. This screening produced numerous hybridizing recombinant phage that contained inserts longer than those previously obtained, including one which was of a size t ...
pDsRed-Monomer-C1 Vector Information
... The Xba I and Bcl I sites are methylated in the DNA provided by Clontech Laboratories, Inc. If you wish to digest the vector with these enzymes, you will need to transform the vector into a dam– host and make fresh DNA. ...
... The Xba I and Bcl I sites are methylated in the DNA provided by Clontech Laboratories, Inc. If you wish to digest the vector with these enzymes, you will need to transform the vector into a dam– host and make fresh DNA. ...
Genomescale models of metabolism and gene expression extend
... prosthetic group synthesis and utilization in the ME-Model. Specifically, for a protein complex to be functional in the MEModel it has to contain the embedded prosthetic groups required for function; while this change in model structure results in some false predictions of essentiality compared with ...
... prosthetic group synthesis and utilization in the ME-Model. Specifically, for a protein complex to be functional in the MEModel it has to contain the embedded prosthetic groups required for function; while this change in model structure results in some false predictions of essentiality compared with ...
Detailed proteome analysis of growing cells of the planctomycete
... unknown proteins RB4405, RB4438, RB4474, RB6428, RB6430, RB8580, RB10934, RB10956, RB11176, and RB12297. Sixty percent of the 200 most abundant proteins on the master gel (contributing to 64.6% of the total spot volume) were encoded by genes that were predicted to be highly expressed (PHX) according ...
... unknown proteins RB4405, RB4438, RB4474, RB6428, RB6430, RB8580, RB10934, RB10956, RB11176, and RB12297. Sixty percent of the 200 most abundant proteins on the master gel (contributing to 64.6% of the total spot volume) were encoded by genes that were predicted to be highly expressed (PHX) according ...
An Essential Role of the Mitochondrial Electron Transport Chain in
... phenformin, were several encoding ETC-related proteins, including complex I subunits (NDUFA11, NDUFB2, NDUFA10, NDUFB9), mitochondrial RNA processing and ubiquinone synthesis enzymes (PDE12 and COQ4), and ETC assembly factors (ACAD9 and SCO2) (Figure 1D, Figure S1B). Unlike genes encoding core ETC c ...
... phenformin, were several encoding ETC-related proteins, including complex I subunits (NDUFA11, NDUFB2, NDUFA10, NDUFB9), mitochondrial RNA processing and ubiquinone synthesis enzymes (PDE12 and COQ4), and ETC assembly factors (ACAD9 and SCO2) (Figure 1D, Figure S1B). Unlike genes encoding core ETC c ...
Over-expression of UDP-glucose pyrophosphorylase in hybrid
... a 270-fold increase in the salicylic acid 2-O-b-Dglucoside (SAG), a compound typically associated with the stress response. These data suggest that while it is possible to alter the allocation of carbon in favour of cellulose biosynthesis, whole plant changes result in unexpected decreases in growth ...
... a 270-fold increase in the salicylic acid 2-O-b-Dglucoside (SAG), a compound typically associated with the stress response. These data suggest that while it is possible to alter the allocation of carbon in favour of cellulose biosynthesis, whole plant changes result in unexpected decreases in growth ...
Supplementary Materials
... Many loci show positive or negative scores in the fitness profiles. The Spearman's rank correlation () between the two transposon libraries (4% and 5.5%) was determined to be 0.58 (p-value<2.2e-16). The overexpression samples showed a value of 0.72. These significant correlations for both cases s ...
... Many loci show positive or negative scores in the fitness profiles. The Spearman's rank correlation () between the two transposon libraries (4% and 5.5%) was determined to be 0.58 (p-value<2.2e-16). The overexpression samples showed a value of 0.72. These significant correlations for both cases s ...
Transcriptome analysis reveals unique C4
... the improvement of ArA level. Therefore, genes encoding fatty acid desaturases and elongase of this microalga have been characterized, and some routes were determined by heterologous expression of these genes in model organisms [10,17-19]. Carotenogenesis pathways in microalgae are similar to those ...
... the improvement of ArA level. Therefore, genes encoding fatty acid desaturases and elongase of this microalga have been characterized, and some routes were determined by heterologous expression of these genes in model organisms [10,17-19]. Carotenogenesis pathways in microalgae are similar to those ...
Evolution of codon usage bias in Drosophila
... Could mutation bias account for codon usage bias in Drosophila? For three reasons this seems to be very unlikely. First, Drosophila have no isochores (18). As noted above, very tightly linked genes can be very different in codon usage bias, notably Adh and Adhr, which are only a few hundred base pai ...
... Could mutation bias account for codon usage bias in Drosophila? For three reasons this seems to be very unlikely. First, Drosophila have no isochores (18). As noted above, very tightly linked genes can be very different in codon usage bias, notably Adh and Adhr, which are only a few hundred base pai ...
L - bioweb: molecular modelling group
... Darwin and homology • “The natural system is based upon descent with modification .. the characters that naturalists consider as showing true affinity (i.e. homologies) are those which have been inherited from a common parent, and, in so far as all true classification is genealogical; that communit ...
... Darwin and homology • “The natural system is based upon descent with modification .. the characters that naturalists consider as showing true affinity (i.e. homologies) are those which have been inherited from a common parent, and, in so far as all true classification is genealogical; that communit ...
Molecular Characterization of –Lactalbumin Folding Variants That
... properties at physiological conditions. The results suggest differences in biological properties between folding variants of a-lactalbumin. ...
... properties at physiological conditions. The results suggest differences in biological properties between folding variants of a-lactalbumin. ...
File
... 4. At which stage is it the most difficult to tell the embryos apart? (I, II, or III) I 5. Describe at least one similarity in the structure of these embryos Eyes, spinal cord, begin life with a tail 6. How do these similarities support the evidence of ancestry? The embryo begins with very similar c ...
... 4. At which stage is it the most difficult to tell the embryos apart? (I, II, or III) I 5. Describe at least one similarity in the structure of these embryos Eyes, spinal cord, begin life with a tail 6. How do these similarities support the evidence of ancestry? The embryo begins with very similar c ...
Consequences of Stop Codon Reassignment on
... a million of being more minimized than the standard code. In their study, Freeland et al. (2000) used the PAM74100 matrix (Benner et al. 1994) to determine the distance between a pair of amino acids. PAM stands for point accepted mutations, for example, a PAM1 matrix is determined from the alignment ...
... a million of being more minimized than the standard code. In their study, Freeland et al. (2000) used the PAM74100 matrix (Benner et al. 1994) to determine the distance between a pair of amino acids. PAM stands for point accepted mutations, for example, a PAM1 matrix is determined from the alignment ...
Insilico Studies on Taste Receptor Gene (Tas2r38) and Tas2r38
... Taste Receptor 2 member 38 is a protein that in humans are encoded by the TAS2R38 gene [2],[3]. Three common Single Nucleotide Polymorphisms (SNPs) were identified in this gene, which is at base pairs 145 (C-G), 785 (C-T) and 886 (G-A), resulting in 3 amino acid substitutions at codons P49A, A262V, ...
... Taste Receptor 2 member 38 is a protein that in humans are encoded by the TAS2R38 gene [2],[3]. Three common Single Nucleotide Polymorphisms (SNPs) were identified in this gene, which is at base pairs 145 (C-G), 785 (C-T) and 886 (G-A), resulting in 3 amino acid substitutions at codons P49A, A262V, ...
PREDICTION OF THE INTERACTION OF HIV
... resistance, together with toxicity problems, requires the discovery and development of new classes of anti-AIDS drugs.7–9 The HIV-1 integrase, responsible for the integration of the newly synthesized double-stranded viral DNA into the host genomic DNA, is a new and important target of potential clin ...
... resistance, together with toxicity problems, requires the discovery and development of new classes of anti-AIDS drugs.7–9 The HIV-1 integrase, responsible for the integration of the newly synthesized double-stranded viral DNA into the host genomic DNA, is a new and important target of potential clin ...
patrick_tb_ch17
... other options are not valid. The structure could be phosphorylated to the active triphosphate if it reached infected cells, but most of it will get hydrolysed before it does so. The drug is no more polar or hydrophobic than cidofovir, and so this is not a disadvantage either. Page reference: 447 a. ...
... other options are not valid. The structure could be phosphorylated to the active triphosphate if it reached infected cells, but most of it will get hydrolysed before it does so. The drug is no more polar or hydrophobic than cidofovir, and so this is not a disadvantage either. Page reference: 447 a. ...
Article, Discoveries Variation in mutational robustness between
... their underlying evolutionary rationale, we used highly sensitive competition experiments to measure the DFE of random mutations for three genes from different protein classes in their native context to investigate if the high robustness of RPs is an exception and if any general properties of the DF ...
... their underlying evolutionary rationale, we used highly sensitive competition experiments to measure the DFE of random mutations for three genes from different protein classes in their native context to investigate if the high robustness of RPs is an exception and if any general properties of the DF ...
Effect of essential and non-essential amino acid addition to a
... the re-utilization of AA present in the AA pool. It has been repeatedly demonstrated that small supplements of sulphur amino acids and threonine to an N-free diet significantly reduce urinary N excretion and improve N retention (Yokogoshi and Yoshida, 1976, 1981) and therefore these AA are the most ...
... the re-utilization of AA present in the AA pool. It has been repeatedly demonstrated that small supplements of sulphur amino acids and threonine to an N-free diet significantly reduce urinary N excretion and improve N retention (Yokogoshi and Yoshida, 1976, 1981) and therefore these AA are the most ...
Endogenous retrovirus
Endogenous retroviruses (ERVs) are endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome (lower estimates of ~1%). ERVs are a subclass of a type of gene called a transposon, which can be packaged and moved within the genome to serve a vital role in gene expression and in regulation. Researchers have suggested that retroviruses evolved from a type of transposable gene called a retrotransposon, which includes ERVs; these genes can mutate and instead of moving to another location in the genome they can become exogenous or pathogenic. This means that all ERVs may not have originated as an insertion by a retrovirus but that some may have been the source for the genetic information in the retroviruses they resemble.