Alignments and probabilistic hidden Markov models (HMMs) of structured domains found in GCNA family members.

(A) HMM of GCNA protease domain with its HExCH active site. (B) HMM of the characteristic C2C2 zinc finger found in the GCNA family. (C) Alignment of GCNA HMG boxes with the HMMs from Pfam HMGs (a conglomerate of many types of HMG boxes) and GCNA HMGs. Canonical HMG boxes are shown for comparison. Residues identical in 70% of the sequences are shaded black; similar residues are gray. (D) Secondary structure prediction of GCNA HMG boxes showing the two predicted alpha helices (orange). Most GCNA proteins terminate before the third helix of canonical HMG boxes, but a third helix may form in some species. HMMs used for ortholog discovery can be found in Figure 4—figure supplement 1—source data 1—source