Computational protocol: Identification of Multiple Soluble Fe(III) Reductases in Gram-Positive Thermophilic Bacterium Thermoanaerobacter indiensis BSB-33

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Protocol publication

[…] Pairwise sequence similarity was determined using BLASTP ( Amino acid sequences of proteins were aligned using ClustalW2 ( Three-dimensional (3D) structures of proteins were built from amino acid sequences using automated homology modeling program ESyPred3D that is based on a very efficient alignment strategy and the MODELLER package to build the final structural model [,]. 3D structures were compared using DaliLite [,] and PDBeFold [,]. For visualization and superposition of 3D structures UCSF Chimera v.1.8 downloaded from was used []. Functional domains were searched by InterProScan ( […]

Pipeline specifications

Software tools BLASTP, Clustal W, ESyPred3D, DaliLite, PDBeFold, UCSF Chimera, InterProScan
Application Protein structure analysis
Organisms Thermus scotoductus, Desulfovibrio desulfuricans
Chemicals Amino Acids, Iron