Table 8 GO terms are not suitable for protein residue annotation. The presented examples demonstrate that predicted GO terms are not always suitable for protein residue annotation. The prediction of GO terms was done with an information theory based parser [34].
From: Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb
| Â | Â | Annotation | |
|---|---|---|---|
Example | Sentence | Manual | GO |
1 | "The catalytic mechanism of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase and the other aldehyde dehydrogenases resembles a thioester mechanism involving the universally conserved cysteine 298 (pea GAPN)." (PMID:9461340) | thioester mechanism, conserved cysteine | glyceraldehyde-3-phosphate dehydrogenase (NADP+)(phosphorylating activity), glyceraldehyde-3-phosphate biosynthesis, glyceraldehyde-3-phosphate catabolism, phosphoglycerate dehydrogenase activity |
2 | "However, mutations of a key residue, His48, show significant deviation from the relationship, implying a role for the side chain in protection of the complex from hydroxide attack." (PMID:2690955) | protection of the complex from hydroxide attack | AT DNA binding, tRNA, tyrosine tRNA ligase activity |
3 | "Second, this reactive cysteinyl residue, which is required for L-cysteine desulfurization activity, was identified as Cys325 by the specific alkylation of that residue and by site-directed mutagenesis experiments." (PMID:81615929) | L-cysteine desulfurization activity | pyridoxal biosynthesis, phosphate binding, mutagenesis, nitrogenase activity, L-alanine biosynthesis, pyridoxal phosphate binding |