The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny.

ABSTRACT: Intrinsically disordered proteins (IDPs) are proteins that lack a stable 3D structure but maintain a biological function. It has been frequently suggested that IDPs are difficult to align because they tend to have fewer conserved residues compared to ordered proteins, but to our knowledge this has never been directly tested. To compare the alignments of ordered proteins to IDPs, their multiple sequence alignments (MSAs) were assessed using two different methods. The first compared the similarity between MSAs produced using the same sequences but created with Clustal Omega, MAFFT, and MUSCLE. The second assessed MSAs based on how well they recapitulated the species tree. These two methods measure the "correctness" of an MSA with two different approaches; the first method measures consistenc

SUBMITTER: Riley AC 

PROVIDER: S-EPMC10343074 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature