Computational protocol: The ineluctable requirement for the trans-iron elements molybdenum and/or tungsten in the origin of life

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Protocol publication

[…] Amino acid sequences of CISM superfamily members were retrieved via BLAST searches on the NCBI-database (http://www.ncbi.nlm.nih.gov) using biochemically or structurally characterized representatives of the subfamilies nitrate reductase (Nar), polysulfide reductase (Psr), formate dehydrogenase-N (Fdh), DMSO reductase (Dms/Dor/Tor), arsenite oxidase (Aro) and arsenate reductase (Arr) as queries. The number of hits used for each major species phylum was limited in order to avoid unreadable trees induced by the strong oversampling of specific classes of prokaryotes in the databases (e.g. proteobacteria or pathogenic actinobacteria). Gene cluster context was assayed by analyzing the genomic environment of each sequence on the respective genome web-pages of the NCBI server.Multiple alignments of recognized subfamilies were automatically produced using Clustal, MEGA, Mafft (http://mafft.cbrc.jp/alignment/software/about.html), Muscle and T-Coffee and in cases subsequently refined with respect to functionally conserved residues using Seaview. The second and third line sequence alignments in were performed using Clustal and T-Coffee, respectively.The ensemble of enzymes for which 3D structures are available were aligned via DeepView (www.expasy.org/spdbv/; see Figure and alignment file in ) [...] NJ-trees were reconstructed using ClustalX and MEGA-4. These two programs yielded tree topologies differing only in a few very late branching orders. The tree shown in and available as phb-file in has been obtained using ClustalX. Gap positions were taken into account. Multiple substitutions were allowed for using Kimura's correction algorithm. Calculated bootstrap values correspond to the frequency of occurrence of nodes in 1,000 bootstrap replicates. […]

Pipeline specifications

Software tools MEGA, MAFFT, MUSCLE, T-Coffee, SeaView, Swiss-PdbViewer, Clustal W
Databases ExPASy
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Molybdenum, Sulfur, Tungsten