Plant metabolic pathway databasesMathematical modeling of plant metabolism offers new approaches to improve the understanding of complex biological processes. In this chapter an overview of resources and tools available for the reconstruction of stoichiometric models and their constraint-based analysis is ...
The Plant Metabolic Network (PMN, www.plantcyc.org) houses a growing set of plant metabolic pathway databases. In 2012, new versions of the core resources, PlantCyc (version 7.0), AraCyc (10.0), and PoplarCyc (5.0) were joined by CornCyc, GrapeCyc, SoyCyc, CassavaCyc, MossCyc, Selagin...
Pathway databases provide information about the role of chemicals, genes, and gene products in the form of or RNA, their interactions leading to the formulation of metabolic, , regulatory, and reactions. The reactions can then be tethered by the principle of inputs and outputs of one or more...
The proteins were mapped to their corresponding metabolic pathway(s), based on programs available at the PlantPRreS website (www.Proteome.ir), which informed with respect to the involvement of proteins identified in other experiments (Mousavi et al., 2016). The VANTED platform was used to ...
Metabolic pathway databases for plant research. Plant Physiology. 2005, 138 (1): 27-37. 10.1104/pp.105.060376. PubMed CAS PubMed Central Google Scholar Kanehisa M, Goto S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research. 2000, 28 (1): 27-30. 10.1093/nar/28.1.27...
The present study used untargeted metabolomics to reveal for the first time the secondary metabolite changes of walnut roots in response to AMF under drought conditions, and revealed the metabolic mechanism for mycorrhizal enhancement of drought tolerance in walnut. Pathway changes of differential metaboli...
With the exception of the two benzoic acid derivatives (i.e. syringic and gallic acid) all phenolic compounds examined in this study derive from the phenylpropanoid pathway. Phenylpropanoids comprise nearly 20 % of total carbon in the terrestrial biosphere [66] and more than 7000 different ...
metabolic changes. Interestingly AACT1 is localized in peroxisomes, indicating a possibly different metabolic role of AACT1 relative to AACT216. The next enzyme in the pathway is 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS). Knockdown mutation ofHMGSresults in deficient formation of the pollen ...
metabolic changes, such as changes in the nutrients stored inside the seeds, proteins and carbohydrates, which provide the seeds with the energy required for germination and growth [12]. During the germination process, the pentose phosphate pathway is converted from the tricarboxylic acid cycle ...
[10,11], can be used instead of BLAST. A comprehensive comparison of these tools is out of the scope of this manuscript. Some databases or tools provide pre-computed homologous genes [8,12]. Additional steps must be performed to ensure that the gene ids from OMA [10], OrthoFinder [11]...