Rooting and bootstrap analysis

Construction and analysis of a tree containing paralogies.

I searched for homologues of the protein CLPX_ECOLI within chosen bacteria proteoms. The proteoms were downloaded:

cat /P/y16/term4/Proteomes/mnemonic.fasta >> proteoms_pr3.fasta

Then I made a database for blast searching:

makeblastdb -in proteoms_pr3.fasta -out proteoms_pr3_db.fasta -dbtype prot

Then I conducted searching for homologues by BLASTP (installed on kodomo)

blastp -query CLPX_ECOLI.fasta -db proteoms_pr3.fasta -evalue 0.001 -out blast2.out -outfmt 7

As a result the file blast2.out was received (for some reason there are found two findings of the protein HSLU in each species). All findings was downloaded by Uniprot service and aligned by program Muscle by Jalviewer. The alignment you can see here. The phylogenetic tree was build by UPGMA by MEGA.

Terms

Homologues are proteins which have the same genetic predecestor.

Ortologues are homologues which separated as a result of species formation (they are homologues in organisms of different species).

Paralogues are homologues which separated as a result of gene duplication (they are homologues in organisms of the same species).

Tree imagine

There is phylogenetic tree of CLPX's homologues in chosen bacteria. A few examples of the last node before ortologues' separation is marked by red circle - species formation. A few examples of paralogues are marked with blue line (in YERPS) and green lines (in BRADU) - gene duplication.

Term 4

← Pr 1 → Pr 3