PMC:4502367 / 15723-17238 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502367","sourcedb":"PMC","sourceid":"4502367","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502367","text":"Functional annotation\nAutomated functional annotations of the predicted proteins of Z. tritici, Z. pseudotritici, Z. ardabiliae, and Z. brevis were performed as previously described by Grandaubert et al. (2014). Using a combination of BLAST and InterProScan (Quevillon et al. 2005), predicted proteins of each of the four species were categorized into three classes. The first class included proteins with no significant BLAST hit and with no known protein domain identified by InterProScan. These proteins were classified as “predicted proteins,” i.e., predictions with no functional support. This class contained an excess of species-specific genes. The second class, termed “hypothetical proteins,” included proteins with at least one domain identified by InterProScan in the InterPro or Pfam databases (Hunter et al. 2012; Coggill et al. 2008) or that fulfilled the BLAST result criteria defined by Grandaubert et al. (2014) and for which the description indicated “hypothetical protein” in more than 90% of the BLAST hits. Globally, this class contained predictions with poor functional evidence likely corresponding to conserved proteins among several organisms but with no defined functions. The third class included predictions that fulfilled the BLAST result conditions with at least one domain from the InterPro or Pfam database corroborating by the consensus BLAST description. This class was termed the “similar to function” and included well-conserved proteins with defined functions in many organisms.","divisions":[{"label":"title","span":{"begin":0,"end":21}}],"tracks":[{"project":"2_test","denotations":[{"id":"25917918-25306241-43386558","span":{"begin":205,"end":209},"obj":"25306241"},{"id":"25917918-15980438-43386559","span":{"begin":276,"end":280},"obj":"15980438"},{"id":"25917918-22096229-43386560","span":{"begin":821,"end":825},"obj":"22096229"},{"id":"25917918-25306241-43386561","span":{"begin":923,"end":927},"obj":"25306241"}],"attributes":[{"subj":"25917918-25306241-43386558","pred":"source","obj":"2_test"},{"subj":"25917918-15980438-43386559","pred":"source","obj":"2_test"},{"subj":"25917918-22096229-43386560","pred":"source","obj":"2_test"},{"subj":"25917918-25306241-43386561","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#daec93","default":true}]}]}}