Rooting and bootstrap

Here we can see phylogenetic tree of selected bacteria, builded with Muscle with defaults and NJ method. All of the proteins selected with sufficient e-values.

We can see the duplication (marked with pepper) occurred and now 2 types of proteins are divided: ClpX protein and HsIU--HsIV peptidase ATPase subunit. So HsIU--HsIV peptidase ATPase subunit from Pasteurella multocida and HsIU--HsIV peptidase ATPase subunit from Haemophilus influenzae are paralogs with ClpX proteins in that organisms. Also, we can see the orthologs (Yersinia pestis and Serratia proteamaculans ClpX, Shewanella denitrificans and Escherichia coli ClpX, Haemophilus influenzae and Pasteurella multocida ClpX. All of them appeared as a result of speciation). Also, we can see that another duplication happens, when sigma-54 interaction domain protein in emerged Yersinia pestis.

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© Gumerov Ruslan, 2017