%0 Journal Article
%T Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157
%A Nicole S Little
%A Taylor Quon
%A Chris Upton
%J Microbial Informatics and Experimentation
%D 2011
%I BioMed Central
%R 10.1186/2042-5783-1-12
%X By using sensitive database searches for similarity, we observed that gene 157 of CRV-strain Zimbabwe (CRV-ZWE) encodes a protein with a domain that is predicted to bind dsRNA. Domain characterization supported this prediction, therefore, we tested the ability of the Robetta protein structure prediction server to model the amino acid sequence of this protein on a well-characterized RNA binding domain. The model generated by Robetta suggests that CRV-ZWE-157 does indeed contain an RNA binding domain; the model could be overlaid on the template protein structure with high confidence.We hypothesize that CRV-ZWE-157 encodes a novel poxvirus RNA binding protein and suggest that as a non-core gene it may play a role in host-range determination or function to dampen host anti-viral responses. Potential targets for this CRV protein include the host interferon response and miRNA pathways.Crocodilepox virus (CRV) is an unclassified member of the Poxviridae family and its complete genome spans 190,054 base pairs [1]. The genome of this species is approximately 61.1% G+C, similar to the genomes of molluscum contagiosum virus (MCV) and the ORF-like viruses. This relatively high G+C% distinguishes these 3 groups of viruses from other poxviruses; MCV and ORF are in separate genera, and it is likely that CRV will also be placed into a separate genus when officially classified. It is not clear what has driven the genomes of these 3 groups of viruses to become relatively GC-rich while other poxviruses have drifted towards a high A+T content. It is important to note that although an overall A+T% is often used to characterize poxvirus genomes, the individual genes in the viruses vary widely in nucleotide composition; for example CRV and vaccinia virus (VACV) genes range in A+T composition from 24-56% and 54-73%, respectively.The level of conservation between the ortholog sets from viruses in the various poxvirus genera varies greatly (25-50% aa identity), this reflects varying structur
%K Crocodilepox
%K vaccinia
%K poxvirus
%K dsRNA-binding protein
%K HHpred
%K virus
%K interferon
%K Robetta
%U http://www.microbialinformaticsj.com/content/1/1/12