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Pipeline publication

[…] atterns of co-occurrence and/or colocalization of its members with other protein families using the set of tools for comparative genome analysis available in SEED () within the functional and genomic contexts provided by the subsystem “Heme Biosynthesis: protoporphyrin-, coproporphyrin- and siroheme-dependent pathways” ( Phylogenetic distribution of the HemX protein family was mapped onto the tree of life (), and protoheme biosynthetic pathway analysis was adapted from reference ., The HemX multiple sequence alignment was KEGG ClustalW ( [accessed March 2017]) () using Staphylococcus aureus strain Newman, Staphylococcus epidermidis strain ATCC 12228, Bacillus anthracis strain Sterne, Chlorobium tepidum strain TLS, Aquifex aeolicus strain VF5, Desulfovfibrio vulgaris strain DP4, and Geobacter sulfurreducens strain PCA. The transmembrane domains depicted were predicted by MEMSAT3 (; accessed March 2017) as described previously (). All models were confirmed using TMHMM 2.0 ( [accessed March 2017]) (), and predictions were matched across prediction servers, with the exception of Chlorobium tepidum, which TMHMM2.0 predicts to have seven rather than eight transmembrane domains., All data analysis and statistical tests were performed using GraphPad Prism 6 software. Replicate numbers and statistical tests for each experiment are listed in the figure legends., Citation Choby JE, Grunenwald CM, Celis AI, Gerdes SY, DuBois JL, Skaar EP. 2018. Staphylococcus aureus HemX modulates glutamyl-tRNA reductase abundance to regulate heme biosynthesis. mBio 9:e02287-17., We thank Lars Hederstedt (Lund University) and members of the Skaar laboratory for their critical evaluation of the manuscript. We thank Victor Torres (New York University) for the gift of strains and […]

Pipeline specifications

Software tools Clustal W, MEMSAT, TMHMM