Computational protocol: Expression of Phi11 Gp07 Causes Filamentation in Escherichia coli

Similar protocols

Protocol publication

[…] Genome databases in NCBI (http://www.ncbi.nlm.nih.gov/) and Pfam (http://pfam.sanger.ac.uk/) were used for bioinformatics analysis of Gp07. EMBOSS programs (https://www.ebi.ac.uk/Tools/emboss/) were used for different bioinformatics analyses like molecular weight determination, charge and presence of different amino acid. Sequence similarity search was carried out by BLAST server (http://www.blast.ncbi.nlm.nih.gov/blast/Blast.cgi). The search for Phi11 gp07 gene was carried out using BLASTP in different databases in Caudovirales order and 50% or more identity was taken as the threshold []. Sequences similar to the gp07 of Phi11 were detected from different non-redundant (NR) protein sequence databases by BLAST (blastp) program 2.2.32+. Alignment of full-length Gp07 protein was performed by Clustal Omega program 1.2.1 (http://www.ebi.ac.uk/Tools/msa/clustalo/). Using all the proteins which shared 50% identity to the Phi11 Gp07, a dendrogram was constructed using ClustalW2 Phylogeny program (https://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/) with neighbor-joining method. […]

Pipeline specifications

Software tools EMBOSS, BLASTP, Clustal Omega, Clustal W
Databases Pfam
Application Phylogenetics
Organisms Escherichia coli
Chemicals Amino Acids