The HA1 domain in which putatively positively selected sites were found was reported, using the alignment of Yang et al. [ 56] in which portions of the influenza HA corresponding to the fusion domain, vestigial esterase domain and receptor binding domain were identified.
CENH3-binding domains were identified by comparing the ChIPed and input data using SICER (Zang et al. 2009), which is designed to identify ChIP-enriched signals that tend to form specific subdomains.
Within some extensions, several known or predicted DNA-binding domains were identified (to be published elsewhere), however only two pairs of MTase sequences were found that fit the criteria of similarity between the AdoMet-binding subdomain, the active site subdomain, and the TRD, without conservation of their co-linearity.
A protein, VC1059, annotated as a short chain dehydrogenase containing an NADPH binding domain, was identified in the active fraction.
A helix-turn-helix motif, the TFIIB recognition element (BRE) binding domain, was identified in every new TFB protein with a sequenced carboxy-terminus [ 31].
Interestingly, two genes coding for proteins with RNA-binding domains are identified, one of which has a pumilio domain suggesting a role in the negative regulation of translation [ 37].
Cortactin splice variants affecting this F-actin-binding domain were identified not only in mammalians, but also in amphibians, fishes and birds.
The four hypervariable regions in the acceptor-binding domain were identified by multiple sequence alignment of all 91 vertebrate UGT1 variable polypeptides and the corresponding regions of 35 UGT2 proteins in conjunction with analyzing patterns of nt substitutions by the codeml program (see below).
