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HMSS2: an advanced tool for the analysis of sulfur metabolism, including organosulfur compound transformation, in genome and metagenome assemblies
  • Tomohisa Tanabe,
  • Christiane Dahl
Tomohisa Tanabe
Rheinische Friedrich-Wilhelms-Universit├Ąt Bonn

Corresponding Author:[email protected]

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Christiane Dahl
Rheinische Friedrich-Wilhelms-Universit├Ąt Bonn
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Abstract

The global sulfur cycle has implications for human health, climate change, biogeochemistry, and bioremediation. The organosulfur compounds that participate in this cycle not only represent a vast reservoir of sulfur, but are also used by prokaryotes as sources of energy and/or carbon. Closely linked to the inorganic sulfur cycle, it involves the interaction of prokaryotes, eukaryotes, and chemical processes. However, ecological and evolutionary studies of the conversion of organic sulfur compounds are hampered by the poor conservation of the relevant pathways and their variation even within strains of the same species. In addition, several proteins involved in the conversion of sulfonated compounds are related to proteins involved in sulfur dissimilation or turnover of other compounds. Therefore, the enzymes involved in the metabolism of organic sulfur compounds are usually not correctly annotated in public databases. To address this challenge, we have developed HMSS2, a profiled Hidden Markov Model-based tool for rapid annotation and synteny analysis of organic and inorganic sulfur cycle proteins in prokaryotic genomes. Compared to its previous version (HMS-S-S), HMSS2 includes several new features. HMM-based annotation is now supported by non-homology criteria and covers the metabolic pathways of important organosulfur compounds, including dimethylsulfpopropionate, taurine, isethionate, and sulfoquinovose. In addition, the calculation speed has been increased by a factor of four and the available output formats have been extended to include iTol compatible datasets, and customised sequence FASTA files
10 May 2023Submitted to Molecular Ecology Resources
12 May 2023Submission Checks Completed
12 May 2023Assigned to Editor
12 May 2023Review(s) Completed, Editorial Evaluation Pending
22 May 2023Reviewer(s) Assigned
05 Jul 2023Editorial Decision: Revise Minor
07 Jul 20231st Revision Received
10 Jul 2023Submission Checks Completed
10 Jul 2023Assigned to Editor
10 Jul 2023Review(s) Completed, Editorial Evaluation Pending
17 Jul 2023Editorial Decision: Accept