Our improved classification scheme (Figure 10) and the differences we highlight, specifically in respect to the widely used synteny based classification, provide a number of testable predictions regarding which Hox-proteins should be functionally most similar across the major model organisms.
When only GO annotations were taken into account, ICA69 was the protein functionally most similar to VAMP2, primarily, because both proteins are annotated with the term secretory granule membrane.
Despite apparent differences in organization, the amino acid sequences encoded by all six G. lovleyi pce-genes have their most similar homologs among the functionally characterized pce-gene clusters from Desulfitobacterium hafniense strain Y51 (AB070709), D. hafninese strain TCE1 (and39608), anD.D. restrictus (AJ439607).
71.11% of all functionally annotated proteins were most similar to the mammalian species human, mouse, rat and bovine, 11.02% to fungal proteins, 10.85% to insects, whilst 6.35% displayed the highest similarity to miscellaneous eukaryotic organisms.
Functionally, therefore, GAT-1 seems most similar to ExuT.
Notably, these two glycine doublets are conserved in most V4R domains as well, suggesting the existence of a similar, functionally important structural arrangement.
This results in so-called in-paralogs, which may inject additional bias if, compared to the query protein, the most functionally similar of the set is not the most similar at the sequence level.
Amphioxus Hox13 is most similar to vertebrate Hox11, though the sequences have noticeably diverged and a fully functionally equivalent protein should not be expected.
So using NATALIEQ, we find that FZD1 may functionally be more related to FBpp0077788 than its sequence-wise most similar counterpart FBpp0075485.
First, protein sequence comparison showed that Tc-MYBPA was most similar to the grape PA transcriptional regulator VvMYBPA1 and shared the conserved motifs of all the other functionally characterized R2R3-MYB PA synthesis regulators.
