Microbial metabolism in metagenomes

This repository contains hidden Markov models (HMMs) for annotating protein-coding genes in microbial metagenomes and metagenome-assembled genomes.

HMM sets

• sulfur disproportionation: yedE-like, tusA, dsrE-like, chp1, chp2
• denitrification: narG, narH, napA, nirK, nirS, cnor, qnor, bnor, snor, nosB, nosZI, nosZII

Sulfur disproportionation

sulfur_hmms contains HMMs for annotation of genes in the YTD gene cluster putatively involved in sulfur disproportionation.

For info on the YTD gene cluster: Umezawa et al. Disproportionation of inorganic sulfur compounds by a novel autotrophic bacterium belonging to Nitrospirota. Syst. Appl. Microbiol. (2020).

For info on the HMMs: Bell et al. Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. ISME J (2022).

Denitrification

denitrification_hmms contains HMMs for annotation of denitrification genes in members of the phylum Bacillota.

Denitrification HMMs can be used individually or as a denitrification gene set. An example script to run the HMM gene set on a directory of genome amino acid files (.faa) with HMMER is included.

Publication at: Bell et al. Denitrification genotypes of endospore-forming Bacillota. ISME Communications (2024).