Computational protocol: Dimeric chlorite dismutase from the nitrogen‐fixing cyanobacterium Cyanothece sp. PCC7425

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Protocol publication

[…] Analysis of sequenced cyanobacterial genomes was performed using public databases (, For the reconstruction of a phylogenetic tree, the amino acid sequences of 29 Cld‐like proteins and of 19 functional Clds were extracted from the NCBI database and aligned by using the MUSCLE algorithm (Edgar, ) with the following settings: gap open −2.9, gap extend 0, hydrophobicity multiplier 1.2, maximum iterations 8, clustering method UPGMB. A phylogenetic tree was then calculated by applying the maximum likelihood algorithm with the following parameters: Jones–Taylor–Thornton model, gamma distribution set to 3, complete deletion of gaps/missing data, and 1000 bootstrap iterations. Sequence alignment and tree reconstruction were performed using the MEGA6 software (Tamura et al., ).Analysis of putative signal sequences was performed with SignalP 4.1 (Petersen et al., ), TatP 1.0 (Bendtsen et al., ) and Secretome 2.0 (Bendtsen et al., ) ( […]

Pipeline specifications

Software tools MUSCLE, MEGA, SignalP, TatP
Databases ExPASy
Applications Phylogenetics, Protein sequence analysis, Nucleotide sequence alignment
Organisms Escherichia coli
Chemicals Heme, Manganese, Nitrogen, Oxygen, Superoxides