Computational protocol: Posttranslational modification of a vanadium nitrogenase

Similar protocols

Protocol publication

[…] Protein sequences were accessed from the GenBank database and input in the ClustalW alignment tool (Larkin et al. ; Benson et al. ). Phylogenetic trees were built using Mega5 software (Tamura et al. ). Protein sequences were aligned using the ClustalW algorithm and phylogenies inferred using the neighbor-joining method after all alignment gaps were deleted (Saitou and Nei ; Larkin et al. ). The bootstrap consensus trees inferred from 500 replicates were taken to represent the evolutionary history of the taxa analyzed (Felsenstein ). Branches corresponding to partitions reproduced in less than 50% bootstrap replicates were collapsed. The evolutionary distances were computed using the p-distance method and are in the units of the number of amino acid differences per site (Nei and Kumar ). […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Bacteria, Rhodopseudomonas palustris CGA009, Rhodopseudomonas palustris
Chemicals Adenosine Diphosphate, Ammonia, Iron, Molybdenum, Nitrogen, Vanadium, Ammonium Compounds