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 (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Amino acid sequences of proteins were aligned using ClustalW2 (http://www.ebi.ac.uk/Tools/msa/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 [, http://www.expasy.org/proteomics/protein_Structure]. 3D structures were compared using DaliLite [, http://www.ebi.ac.uk/Tools/structure/dalilite] and PDBeFold [, http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver]. For visualization and superposition of 3D structures UCSF Chimera v.1.8 downloaded from http://www.cgl.ucsf.edu/chimera was used []. Functional domains were searched by InterProScan (http://www.ebi.ac.uk/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