SMDB
Sulfur Metabolism Genes Integrative Database provides a high quality, manually curated database of genes that are experimentally confirmed to confer sulfur metabolism, fully referenced to the scientific literature. SMDB also includes homologous sequences of sulfur metabolism genes, as the sulfur metabolism genes may differ between species and/or occur in different forms that are not (yet) experimentally investigated. The homologous sequences of genes are generated by sequence similarity searches in public databases, using an uniform cut-off for genes. SMDB provides tools for identification of sulfur metabolism genes in proteins and metagenome. The genes in the databases can be accessed either through the browsing option, where one can browse genes by their name. Using the advanced search option, one may search specifically for pathway e.g. Dissimilatory sulfate reduction genes. The entire database can also be downloaded for off-line analysis of larger datasets.
In a word, we created a manually managed database that primarily gathers most of the publicly available sulfur cycle gene families. A total of 175 gene (sub) families covering 11 sulfur metabolism pathways, including assimilatory sulfate reduction, thiosulfate disproportionation, sulfide oxidation, dissimilatory sulfate reduction, sulfite oxidation, sulfur oxidation, sulfur reduction, tetrathionate oxidation, tetrathionate reduction, thiosulfate oxidation, and organic degradation/synthesis, were recruited in SMDB. SMDB database can be applied to any environmental sample of metagenomic sequencing and supports single sequence analysis.
Shuming Mo, Bing Yan, Tingwei Gao, Jinhui Li, Muhammad Kashif, Jingjing Song, Lirong Bai, Dahui Yu, Jianping Liao & Chengjian Jiang. Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB. Scientific Reports. 2023.13(1): 8126. doi: https://doi.org/10.1038/s41598-023-34995-y