An iron-binding protein common to many external secretions.
The 44 uncharacterised proteins, several of which are apparently nucleic acid (either DNA or RNA) binding proteins (common among small DUF proteins [ 35]) (Additional file 2: Table S2), were selected for further analysis.
It is noteworthy that nuclear proteins and nucleic acid binding proteins are common targets to autoimmunity, and abnormal apoptosis has been associated with autoimmunity [ 38].
In addition, a comparison of the 28 common RNA binding proteins to those identified by recent PAR-CL and PAR-CLIP-seq studies [ 19, 20] demonstrates that 21/28 and 18/28 of these proteins, respectively, demonstrate RNA binding ability including NUDT16L1.
Only three proteins (P46 013, Antigen KI-67; Q09666, Neuroblast differentiation-associated protein AHNAK; Q5SSJ5, Heterochromatin protein 1-binding protein 3) were common to all experimental settings.
The structure of the C-terminal catalytic domain of tRNA splicing endoribonuclease (RNase) EndA is identical to the minimal core of the PD-(D/E XK fold [ 23], yet this protein lacks the Mg2+ binding site common to its cousins that cleave phosphodiester bonds in DNA.
CTCF is one of only a few insulator/chromosomal architectural DNA binding proteins that are known to be common to both insects and vertebrates [ 28, 30, 36, 85].
The unexpected similarity between RPEL and DBP actin contacts close to the subdomain 3 ledge prompted us to perform structure-based sequence alignments with other actin cleft-binding proteins to examine common structural features.
Binding proteins to both sites were characterized by several methods.
The alternative approach to identification of calcium-binding sites common to RTX proteins was to use the HMM-based model for hemolysin-type calcium-binding repeats, the PF00353 from Pfam database release 23.0 (Finn et al., 2006), which is an 18-residue-long model of two calcium-binding sites.
