Mapping replicative protein domains on the NDiV genome.

aOpen reading frame (ORF) 1a and ORF1b nucleotide sequences in NDiV were in silico translated to obtain the encoded polyprotein (pp) sequences 1a and pp1ab. To map domains in these polyproteins, we employed HMMer, HHsearch. The obtained significant hits were mapped back to the genome.bThe proteolytic cleavage sites in the NDiV pp1a/pp1ab remain to be identified. To provisionally assign the mapped domains to mature proteins, the names of non-structural proteins (nsp) in SARS-CoV that are autoproteolytically released from pp1a/pp1ab are shown. Note that all replicative domains mapped in NDiV are located in the canonical positions.cSizes of TM2 and TM3 as determined by TMpred may correspond only to small portions of the respective nsp4 and nsp6 proteins.dPortions of pp1ab that were submitted as targets to profiles searches.eShown is the virus diversity range of a query domain profile: the subfamilies Coronavirinae (corona) and Torovirinae (toro), the family Roniviridae (roni) and the order Nidovirales (nido). The used profiles for 3CLpro, RdRp, ZmHel1, ExoN, NMT and OMT are part of an in-house nidovirus domain profile database. No query (“-”) was used for analyses mediated by TMpred.fE-value for HMMer/HHsearch based on a database size of 12000 according to the size of the Pfam (version 24.0, October 2009); TMpred score otherwise.gThe assignment was done according to a profile-vs-profile search in local mode of the domain flanked by TM2 and TM3 in NDiV against the respective ronivirus profile.hThe assignment was done according to a profile-vs-profile search in global mode of the domain flanked by ExoN and OMT in NDiV and roniviruses against the respective coronavirus.