Computational protocol: A Novel, Molybdenum-Containing Methionine Sulfoxide Reductase Supports Survival of Haemophilus influenzae in an In vivo Model of Infection

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Protocol publication

[…] One thousand and five amino acid sequences of proteins related to Molybdenum containing S- and N-oxide reductases from (see Supplementary Data) were retrieved from GenBank using BLASTP searches with different sulfoxide reductases as the search models. To maximize coverage of this group of proteins, initially several data sets were compiled using E. coli TorA (acc. no. P33225), Rhodobacter capsulatus DorA (acc. no. 1E61), E. coli BisC (acc. no. P20099), E. coli TorZ (acc. no. P46923) and HI TorZ (acc. no. P44798) as input sequences for database searches. Criteria for similarity were a query coverage or 80% or better combined with low e-values for the respective search models. Sequence lists were then combined and duplicates removed. Sequences were aligned using ClustalW as incorporated into the MEGA6.0 software package (), phylogenetic analyses (Neighbor joining, UPGMA, Minimum Evolution) and bootstrapping (500 cycles) were also carried out in MEGA 6.0. […]

Pipeline specifications

Software tools BLASTP, Clustal W, MEGA
Databases BISC
Application Phylogenetics
Organisms Haemophilus influenzae, Homo sapiens, Mus musculus, Escherichia coli
Diseases Asthma, Infection, Respiratory Tract Infections, Pulmonary Disease, Chronic Obstructive