Computational protocol: Phage Orf Family Recombinases: Conservation of Activities and Involvement of the Central Channel in DNA Binding

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Protocol publication

[…] Proteins related to Orf were identified using the TBLASTN and PSI-BLAST algorithms on the non-redundant database at the National Center for Biotechnology Information (NIH, Bethesda, MD). An inclusion threshold of 0.05 was applied in iterative searches to restrict those matches selected in the position-specific weight matrix (PSSM). Sequences were aligned using ClustalW with a Gap Creation Penalty of 10 and Gap Extension Penalty of 1 . Phylogenetic relationships were estimated by the neighborhood-joining method incorporated within the PAUP package . The Jnet protein structure prediction tool on the Jpred server was used to estimate secondary structure features of E. coli DLP12 YbcN and S. aureus φETA Orf20 . The Phyre2 protein fold recognition server is an improved version of 3D-PSSM . […]

Pipeline specifications

Software tools TBLASTN, BLASTP, Clustal W, PAUP*, JPred, Phyre
Applications Phylogenetics, Protein structure analysis, Amino acid sequence alignment
Organisms Escherichia coli