scholarly journals Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Nelson Kibinge ◽  
Shun Ikeda ◽  
Naoaki Ono ◽  
Md. Altaf-Ul-Amin ◽  
Shigehiko Kanaya
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Principal Component ◽  
Analytical Techniques ◽  
Molecular Data ◽  
Amino Acid Index ◽  
Protein Sequence Data ◽  
Physical Attributes ◽  
Acid Index

Progress in the “omics” fields such as genomics, transcriptomics, proteomics, and metabolomics has engendered a need for innovative analytical techniques to derive meaningful information from the ever increasing molecular data. KNApSAcK motorcycle DB is a popular database for enzymes related to secondary metabolic pathways in plants. One of the challenges in analyses of protein sequence data in such repositories is the standard notation of sequences as strings of alphabetical characters. This has created lack of a natural underlying metric that eases amenability to computation. In view of this requirement, we applied novel integration of selected biochemical and physical attributes of amino acids derived from the amino acid index and quantified in numerical scale, to examine diversity of peptide sequences of terpenoid synthases accumulated in KNApSAcK motorcycle DB. We initially generated a reduced amino acid index table. This is a set of biochemical and physical properties obtained by random forest feature selection of important indices from the amino acid index. Principal component analysis was then applied for characterization of enzymes involved in synthesis of terpenoids. The variance explained was increased by incorporation of residue attributes for analyses.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

scholarly journals Genetic diversity of common bean (Phaseolus vulgaris L.) breeding collection in Serbia

Genetika ◽  
2019 ◽  
Vol 51 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Aleksandra Savic ◽  
Milka Brdar-Jokanovic ◽  
Miodrag Dimitrijevic ◽  
Sofija Petrovic ◽  
Milan Zdravkovic ◽  
...  
Keyword(s):  
Common Bean ◽  
Gene Pool ◽  
Gene Diversity ◽  
Principal Component ◽  
Molecular Data ◽  
Phenotypic Traits ◽  
Gene Pools ◽  
Vegetable Crops ◽  
Novi Sad

The characterization of 41 common bean cultivars and landraces from breeding collection of Institute of Field and Vegetable Crops, Novi Sad, Serbia, was done based on phenotypic traits and microsatellite markers. Phenotypic traits were chosen from Bioversity International descriptor list. In addition, main yield components were investigated. Analysis of phaseolin type revealed affiliation of cultivars and landraces to Mesoamerican or Andean gene pool. Cultivars and landraces demonstrated significant diversity level with regard to studied phenotypic traits. Identified variation showed high potential for developing new cultivars with desirable combination of traits. Principal component analysis based on phenotypic traits separated bean cultivars and landraces in two groups, which corresponded to Mesoamerican and Andean determined according to phaseolin type. Putative hybrids, with combination of traits between gene pools were also identified. Analysis of microsatellite data, using twenty-two SSR primer pairs, showed medium gene diversity in studied material. Microsatellite-based cluster analysis separated genotypes in two discrete clusters and several subclusters. No clear separation according to gene pool was found between the clusters, however grouping according to gene pool and patterns of phenotypic variation, following these gene pools, were observed within subclusters. Knowledge on detailed relationships of cultivars and landraces based on phenotypic and molecular data would facilitate identification of candidates for future breeding.

Measurement of the Net Utilization of Heat-Processed Proteins by Means of the Pepsin Digest-Residue (Pdr) Amino Acid Index

1956 ◽  
Vol 60 (4) ◽  
pp. 507-516 ◽  
Author(s):  
A. Leonard Sheffner ◽  
Richard Adachi ◽  
Harry Spector
Keyword(s):  
Amino Acid ◽  
Amino Acid Index ◽  
Acid Index

scholarly journals BIOLOGICAL VALUE OF PROTEINS OF MILK OF SIMMENTAL COWS PRODUCED UNDER CONDITIONS OF INTENSIVE TECHNOLOGY

2021 ◽  
Vol 247 (3) ◽  
pp. 288-292
Author(s):  
L.G. Khromova ◽  
◽  
N.V. Bailova ◽  
A.I. Sychev ◽  
◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Oscillation Amplitude ◽  
Essential Amino Acids ◽  
Acid Number ◽  
Protein Component ◽  
High Concentration ◽  
Biological Value ◽  
Amino Acid Index ◽  
Acid Index

Taking into account modern requirements, the biological value of the protein component of the Simmental breed Krov milk produced under intensive technology has been studied. The amino acid composition of milk proteins was identified by high-performance liquid chromatography. To analyze the biological value of proteins, calculated indicators were used: the amino acid index and the amino acid number (skor) of essential amino acids, taking into account the true digestibility of each of them. As a result of the research, all the essential and interchangeable amino acids and a fairly high concentration of many of them were identified. Among the essential amino acids, the largest amount in the milk samples contained phenylalanine+tyrosine, leucine, lysine, valine, and the smallest-tryptophan, methionine+cysteine. In the aggregate of interchangeable amino acids, the highest saturation was noted for glutamic acid+glutamine, arginine, proline, and the lowest-glycine, alanine. The predominance of interchangeable amino acids was noted in the protein component, which caused a low amino acid index (0.61). The amount of assimilated essential amino acids was higher relative to the reference protein. However, the amino acid score had a wide oscillation amplitude: from 149.6 % for the amino acids phenylalanine + tyrosine to 61.2 and 87.8 %, respectively, for tryptophan and methionine+cysteine, which indicated their imbalance. The essential amino acids tryptophan and methionine+cysteine were limiting, since their amino acid number (skor) is below 100 %.

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