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Related Concept Videos

Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
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Recombinant DNA technology called transgenesis is often used to add a foreign gene or remove a detrimental gene from an organism. Such genetically modified organisms are called transgenic organisms.
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Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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AgBase: supporting functional modeling in agricultural organisms.

Fiona M McCarthy1, Cathy R Gresham, Teresia J Buza

  • 1Department of Basic Sciences, College of Veterinary Medicine, PO Box 6100, Mississippi State University, MS 39762, USA. fmccarthy@cvm.msstate.edu

Nucleic Acids Research
|November 16, 2010
PubMed
Summary
This summary is machine-generated.

AgBase offers enhanced resources for agricultural genomics, providing extensive Gene Ontology (GO) annotations and new tools like GOModeler for hypothesis testing. This redesigned website improves accessibility for functional genomics data modeling.

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Area of Science:

  • Agricultural genomics
  • Functional genomics
  • Bioinformatics

Background:

  • AgBase is a crucial resource for functional genomics data modeling and annotation of agriculturally relevant genomes.
  • Existing resources require improvements in accessibility, ease of use, and search capabilities.

Purpose of the Study:

  • To redesign and enhance the AgBase website for improved accessibility and user experience.
  • To expand functional genomics resources and tools for agriculturally important species.
  • To provide comprehensive Gene Ontology (GO) annotations and facilitate hypothesis testing.

Main Methods:

  • Website redesign focusing on improved accessibility and search functionality.
  • Expansion of dedicated pages for key agricultural species (horse, cat, dog, cotton, rice, soybean).
  • Integration of Gene Ontology (GO) annotations for gene products and agricultural microarrays.
  • Development of new tools, including GOModeler, for hypothesis testing.
  • Hosting of associated databases and genome browsers for agricultural pathogens.

Main Results:

  • Redesigned AgBase website with enhanced accessibility and search.
  • Expanded species coverage with dedicated pages for horse, cat, dog, cotton, rice, and soybean.
  • Provision of over 590,000 Gene Ontology (GO) annotations for 105,000+ gene products across 64 species.
  • Availability of downloadable, species-specific GO annotation files for 18 organisms.
  • Introduction of GOModeler and other new tools to support functional genomics data analysis.

Conclusions:

  • The enhanced AgBase platform significantly improves access to functional genomics data and annotation resources.
  • New tools and expanded datasets empower researchers in agricultural genomics and related fields.
  • AgBase continues to be a vital resource for the agricultural research community, supporting data modeling and hypothesis generation.