How to download KEGG database # download pathway KO genome wget -c http://rest.kegg.jp/list/pathway wget -c http://rest.kegg.jp/list/ko wget -c http://rest.kegg.jp/list/genome # KO list mkdir KO_files cut -f 1 ko | sed 's/ko://' | while read id; do wget -c http://...
Functions of differentially abundant metabolites (DAMs) were annotated using KEGG database (http://www.kegg.jp/kegg/pathway.html) and MetWare metabolite database. 2.3. Measurements of FAAs, lignin, Cu, total N, NH4+-N, NO3--N, TSPs, total phenolics, GSH and MDA in leaves FAAs were ...
2 min). Use 1 mL methanol water to transfer the homogenized sample and repeat the above operation once. Centrifuge for 10 min (7700 rpm, 4 ℃) and 1.2 mL of supernatant was
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Each motif in the database is annotated and curated manually, based on the experimental evidence gathered from publications. The entries themselves are submitted to ELM by filling in two annotation templates designed for motif class and motif instance annotation. In this protocol, we describe the ...
to 2.1 × 105predicted coding sequences of the 78 rMAGS. Per time-point, on average 1.5 × 104 ± 4.5 × 103(s.d.) spectral matches, i.e., on average 94% of all rMAG-associated matches could be assigned to genes with predicted functions, i.e., assigned KEGG ...
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conducted by searching against the following databases: NCBI non-redundant protein (Nr), NCBI non-redundant nucleotide (Nt), Protein family (Pfam), Clusters of Orthologous Groups of proteins (KOG), Swiss-Prot protein (Swiss-Prot), KEGG Ortholog database (KO), and Gene Ontology database (GO)...
P. aeruginosa core metabolism To define the P. aeruginosa core metabolism, all 145 identified metabolites were grouped in metabolic path- ways (KEGG database; http://www.genome.jp/kegg/ kegg2.html). The subgroup of 60 metabolites found in all analysed conditions was considered as ...
Based on the results of PCA and cluster analysis, and enrichment analysis based on the KEGG database was used to compare the differences in the metabolic pathway between the group with a dietary lipid level higher than or equal to 22.8% (22.8% and 29.4% groups) and the group with a ...