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Feature selection was optimized from 5 different methods where the best method chosen for each transporter.
Strict correlations were identified between the complement of particular conformers adopted by a peptide and its bioactivity as a substrate for each transporter.
Like for the other databases, we have integrated multiple data types that include structural features, orthologous relationships, mutant availability, and gene expression patterns for each transporter family (http://ricephylogenomics.ucdavis.edu/transporter/).edu/transporter/
Sugar uptake model following Michaelis Menten kinetics considers the uptake rate of hexose and pentose sugars (e.g. glucose or xylose) for cell growth, product synthesis and for maintenance process, the competitive inhibition between hexoses for each transporter (Pizarro et al. 2007) and the non-competitive inhibition between hexoses and pentoses (Zhang et al. 2009a, b).
The number of rats pooled for each batch and the number of batches analyzed for each transporter are listed in Table 1.
Nucleotide diversity was calculated for each transporter individually, as well as for various groups of genes (e.g., ABC transporters, SLC transporters, transporters highly expressed in the liver and/or the kidney, transporters with high or low promoter activity in in vitro assays).
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In order to estimate the apparent kM for sulfate of each transporter we first analyzed the growth curves of complemented yeasts incubated in liquid media containing different sulfate concentrations (from 0 to 100 μM) as sole sulfur sources (Additional file 5).
For each transporter-embedded membrane patch, lipids overlapping with the protein were removed so that the overall lipid fractions were retained.
For each monomeric transporter or transporter complex in PT, infer the one or more transport reactions that the transporter facilitates.
For each monomeric transporter or transporter complex in P T, infer the one or more transport reactions that the transporter facilitates.
The current density through each transporter for a total of 12 transporters described in Figure 1 is described using two types of current-voltage relationship following previous work [8], [9].
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