The species within the family Pseudonocardiaceae form a distinct clade in
phylogenetic trees based on concatenated protein sequences. Additionally,
Nakamurella multipartite, currently part of the order
Frankiales, also formed a clade with the Pseudonocardiaceae species in 100% of the
bootstrap replications of the phylogenetic trees. A
conserved signature indel has been identified which is found in
N. multipartite and all but one of the Pseudonocardiaceae species. This one-amino-acid insertion in
UMP kinase serves to both provide a
molecular marker for nearly all of the Pseudonocardiaceae and suggests
N. multipartite is closely related to this group. Some evidence also suggests the orders Pseudonocardiales and
Corynebacteriales are closely related. Several conserved signature indels have been identified which are found in both Pseudonocardiales and Corynebacteriales, including a three-amino-acid insertion in a conserved region of
UDP-galactopyranose mutase. This insertion is also present in
N. multipartite and
Geodermatophilus obscurus, another member of Frankiales. Additionally, five conserved signature proteins have been identified which are found only in the orders Pseudonocardiales and Corynebacteriales. Homologs of the proteins are generally found in
N. multipartite and
G. obscurus, providing additional evidence of these two species being closely related to the orders Pseudonocardiales and Corynebacteriales. ==Phylogeny==