Computational protocol: Staphylococcus aureus HemX Modulates Glutamyl-tRNA Reductase Abundance To Regulate Heme Biosynthesis

Similar protocols

Protocol publication

[…] The HemX multiple sequence alignment was KEGG ClustalW (http://www.genome.jp [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 (http://bioinf.cs.ucl.ac.uk; accessed March 2017) as described previously (). All models were confirmed using TMHMM 2.0 (http://www.cbs.dtu.dk [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. […]

Pipeline specifications

Software tools Clustal W, MEMSAT, TMHMM
Databases KEGG
Applications Protein sequence analysis, Membrane protein analysis
Organisms Staphylococcus aureus, Bacteria
Diseases Endocarditis, Infection, Osteomyelitis, Protoporphyria, Erythropoietic, Drug-Related Side Effects and Adverse Reactions
Chemicals Heme, Iron