Computational protocol: Identification and characterization of a 20β-HSDH from the anaerobic gut bacterium Butyricicoccus desmolans ATCC 43058[S]

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Protocol publication

[…] Candidate protein sequences for phylogeny reconstruction were retrieved from NCBI after BLAST using as query the short-chain dehydrogenase/reductase (SDR) family oxidoreductase (WP_051643274.1) from B. desmolans ATCC 43058. Seventy sequences with an identity cutoff of 30% with the 20β-HSDH were selected and aligned using MUSCLE v3.8.31 (). The resulting alignment was manually examined and subsequent phylogeny reconstruction was performed with FastTree v2.1.7 () using the implemented Shimodaira-Hasegawa test to estimate the reliability of each split in the tree. iTOL () was used for visualization of the obtained phylogeny. Deduced protein molecular weight was determined using ExPASy toolkit (). […]

Pipeline specifications

Software tools MUSCLE, FastTree, iTOL
Databases ExPASy
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Escherichia coli
Chemicals Androgens, Androstanes, Hydrocortisone, NAD, Steroids