Comparative Genomic Sequence Analysis

TBLASTN 2.11.0+ [74 (link)] was used to compare TnaA [E. coli], TrpA [E. coli], TrpB [E. coli],TDC [Staphylococcus epidermidis], DDC [Bacillus licheniformis], IpdC [Azospirillum], AofH [Bacillus subtilis], and AldA [E. coli] protein sequences to publicly available sequenced bacterial genomes for isolates GNE6609, GNE6603, GNE6686, and GNE6624 (Genbank: GCF_000011065.1, GCF_900106755.1, GCA_000177015.3, and GCA_003202955.1). Searches yielding high-scoring segment pairs (HSPs) satisfying e value ≤ 0.1 and query coverage ≥ 60% were considered putative evidence of the presence of the query protein in the target genome.

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Mar J.S., Ota N., Pokorzynski N.D., Peng Y., Jaochico A., Sangaraju D., Skippington E., Lekkerkerker A.N., Rothenberg M.E., Tan M.W., Yi T, & Keir M.E. (2023). IL-22 alters gut microbiota composition and function to increase aryl hydrocarbon receptor activity in mice and humans. Microbiome, 11, 47.

Publication 2023

Azospirillum Bacillus licheniformis Bacillus subtilis Bacterial genomes E coli Genome Protein Protein sequences Staphylococcus epidermidis

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Variable analysis

independent variables

TBLASTN 2.11.0+ [74 (link)]

dependent variables

Presence of the query proteins (TnaA [E. coli], TrpA [E. coli], TrpB [E. coli], TDC [Staphylococcus epidermidis], DDC [Bacillus licheniformis], IpdC [Azospirillum], AofH [Bacillus subtilis], and AldA [E. coli]) in the target genomes (isolates GNE6609, GNE6603, GNE6686, and GNE6624)

control variables

Genbank accession numbers of the target genomes: GCF_000011065.1, GCF_900106755.1, GCA_000177015.3, and GCA_003202955.1

controls

Positive controls: Not mentioned
Negative controls: Not mentioned

Annotations

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