Computational protocol: The DUF59 Containing Protein SufT Is Involved in the Maturation of Iron-Sulfur (FeS) Proteins during Conditions of High FeS Cofactor Demand in Staphylococcus aureus

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Protocol publication

[…] The taxonomic distribution of Suf was determined via BLASTp analyses of publically available genome sequences in October of 2011 as part of a previous study []. This distribution of Suf was characterized using the KEGG gene viewer [], with manual verification using BLASTp or using sequence alignments. 1094 genomes out of a total of 1667 genome sequences (65.6% of total) encoded for SufBC. Genomes that encoded for SufBC were then screened for the presence of SufT using BLASTp. sufT was considered to be associated with the suf operon if they were within four open reading frames from sufBC and appeared to be transcribed from a common promoter.SufT sequences were compiled and aligned with ClustalW specifying default parameters []. The aligned sequences were manually truncated to the minimal SufT sequence or positions 1 to 99 of SufT from Thermoplasma acidophilum (Kegg ID: Ta0200). Phyml was used to reconstruct the evolutionary history of the SufT alignment block specifying the Blosum62 substitution model and gamma distributed rate variation []. The topology of the tree was evaluated using Chi2-based likelihood ratio tests. The phylogenetic reconstruction was projected with the Interactive Tree Of Life (Itol) web program [].The N- and C-terminal sequences that were pruned from the alignment block were subjected to BLASTp against the Conserved Domain Database (CDD) using an evalue of 0.01 []. Identified motifs in both N- and C- terminal motifs were compartmentalized into modular structures based on the presence of unique sequence motifs. These N- and C-terminal motifs were mapped onto the SufT phylogenetic tree using the Itol program. Furthermore, SufT was mapped onto a concatenated SufBC phylogenetic tree using the Itol program. The concatenated SufBC tree was constructed as previously described []. […]

Pipeline specifications

Software tools BLASTP, Clustal W, PhyML, iTOL
Databases KEGG
Application Phylogenetics
Organisms Mycobacterium tuberculosis, Staphylococcus aureus, Escherichia coli
Diseases Staphylococcal Infections, Tuberculosis
Chemicals Oxygen, Vancomycin