File containing genomes of all bacteria was created:
cat /P/y16/term4/Proteomes/PSEMY.fasta >> genomes
cat /P/y16/term4/Proteomes/PSEAE.fasta >> genomes
cat /P/y16/term4/Proteomes/POLAQ.fasta >> genomes
cat /P/y16/term4/Proteomes/RHIME.fasta >> genomes
cat /P/y16/term4/Proteomes/PASMU.fasta >> genomes
cat /P/y16/term4/Proteomes/PROMH.fasta >> genomes
cat /P/y16/term4/Proteomes/ECOLI.fasta >> genomes
cat /P/y16/term4/Proteomes/ROSDO.fasta >> genomes
Blast database was created:
makeblastdb -in genomes.fasta -dbtype prot
Blast search was performed:
blastp -query CLPX_ECOLI.fasta -db genomes.fasta -evalue 0.001 -outfmt 7
File for seqret was created. Fasta file containing sequences was generated:
seqret -seq @seq.fasta -out seqs.fasta
Muscle alignment:
muscle -in seqs.fasta -out align.fasta
MEGA
Tree of found homologous proteins was created using UPGMA method by MEGA7 program. Tree is presented in Fig. 1. You can also observe some examples of orthologs and paralogs in this figure.
