Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on Enzyme Commission mapping
Annotation inferences using phylogenetic trees
Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth.
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YciO was identified as a cytosolic protein by biochemical fractionation and mass spectrometry in E. coli K-12
"Here we describe a proteomic analysis of Escherichia coli in which 3,199 protein forms were detected, and of those 2,160 were annotated and assigned to the cytosol, periplasm, inner membrane, and outer membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry."
Protein abundance profiling of the Escherichia coli cytosol.
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YciO was detected in the E. coli cytosolic fraction by mass spectrometry-based protein abundance profiling
"Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample."
Functional annotation of enzyme-encoding genes using deep learning with transformer layers.
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DeepECTransformer predicted YciO has EC 2.7.7.87 (L-threonylcarbamoyladenylate synthase) activity based on sequence features matching TIGR00057 family
"In the case of YciO, which was previously annotated to belong to the SUA5 family, DeepECtransformer predicted its EC number to be EC:2.7.7.87 (L-threonylcarbamoyladenylate synthase) with the prediction score of 0.9108."
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In vitro enzyme assay detected a specific activity of 0.0705 U/mg for L-threonylcarbamoyladenylate synthase activity, but this was not validated in vivo
"The specific activity of YciO was measured to be 0.0705 U mg-1"
Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t<sup>6</sup>A), a universal modification of tRNA
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YciO is described as a paralog lacking the conserved KRSN tetrad (KxR...SxN motif) found in functional TsaC/Sua5 proteins, and does not have the same function. YciO is present in ~54% of 9,176 bacterial genomes analyzed.
NMR-based structural analysis of threonylcarbamoyl-AMP synthase and its substrate interactions.
Slr0006-like proteins - a TsaC/TsaC2/YciO subfamily exclusive to cyanobacteria.
The universal Sua5/TsaC family evolved different mechanisms for the synthesis of a key tRNA modification
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Phylogenomic analysis of the Sua5/TsaC family treats YciO as an inactive bacterial paralog of TsaC, supporting separation of YciO from the canonical TC-AMP synthase/t6A pathway.
"The presence in many bacterial lineages of an inactive paralog of TsaC called Y ciO"
Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.
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YciO is a paralog of TsaC that does NOT perform the same biological function; the in vitro L-threonylcarbamoyladenylate synthase activity (0.14 nM/min) is more than 4 orders of magnitude weaker than TsaC (2.8 uM/min) and represents residual ancestral/promiscuous activity
"the activity reported (0.14 nM/min TC-AMP production rate) for E. coli YciO is more than 4 orders of magnitude weaker than that of E. coli TsaC (2.8 μM/min) at the same enzyme concentration and similar reaction conditions"
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YciO possesses a large conserved positively charged surface (absent in TsaC) predicted to interact with RNA, and yciO genes colocalize with rnm genes encoding RNase AM (rRNA maturation enzyme)
"the structure of YciO exhibits a large positively charged surface predicted to interact with RNA"
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In vivo experiments show YciO cannot substitute for TsaC function; the DeepECTransformer EC 2.7.7.87 prediction was given a confidence score of 0 (refuted) by expert curation
"YciO does not perform the same function as TsaC/Susa5 in vivo experiments"
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This is a textbook example of paralog incorrect (PLI) annotation error, where in vitro promiscuous activity does not reflect biological function
"in vitro activity alone is not sufficient to validate the function of a protein in vivo"
OpenScientist hypothesis report for yciO L-threonylcarbamoyladenylate synthase activity
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OpenScientist judged the TC-AMP synthase activity a vestigial in vitro paralog activity, not the physiological function of YciO.
"**different InterPro subfamilies** (YciO: IPR052532; TsaC subfamily: IPR023535)"