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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Large-scale proteomics study identifying YjdM in the cytosolic fraction of 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.
Functional annotation of enzyme-encoding genes using deep learning with transformer layers.
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DeepECtransformer predicted EC:3.11.1.2 for YjdM with score 0.6103
"YjdM was predicted by DeepECtransformer to have the EC number EC:3.11.1.2 (phosphonoacetate hydrolase). The specific phosphonoacetate hydrolase activity of YjdM obtained by enzyme assay was 139.85 U mg-1"
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In vitro assay showed phosphonoacetate hydrolase activity at 139.85 U/mg
"The reaction mixture for YjdM is composed of 94 μl of 50 mM Tris-HCl (pH 8.0), 2 μl of 10 mM phosphonoacetic acid, and 4 μl of the purified his-tagged YjdM. The enzyme reaction was carried out for 30 min at 35 °C."
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Training sequence with highest similarity to YjdM had different EC number (EC:2.7.7.6)
"for YjdM, predicted by the neural network as EC:3.11.1.2 with a prediction score of 0.6103, the training sequence with the highest sequence similarity had a different EC number (C9Y1B8_CROTZ; EC:2.7.7.6)"
Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli.
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Disruption of yjdM (phnA) has no effect on phosphonate metabolism in E. coli B strains
"The construction of these plasmids showed that phnA and phnB have no role in Pn metabolism."
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Refuted initial report linking yjdM to phosphonate catabolism
"The construction of these plasmids showed that phnA and phnB have no role in Pn metabolism. Also, these plasmids were employed to introduce nonpolar phnD::lacZ and phnD::uidA fusions into the chromosome"
Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B.
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Original cloning and sequencing of the phn locus including yjdM (phnA)
"Seventeen open reading frames (phnA to phnQ) were identified in one transcriptional direction and five open reading frames in the divergent direction"
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Named yjdM as phnA based on genomic proximity to phn operon
"A Pho box-like promoter sequence is also found upstream of the gene cluster starting at phnA"
Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi.
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Metcalf and Wanner showed phn operon is PhoB/PhoR dependent and induced ~100-fold under phosphate limitation. phnA (yjdM) is not essential for the canonical E. coli phosphonate utilization phenotype.
"genetic analyses supported phnC-phnP as the complete set required for phosphonate utilization, implying phnA is not essential"
The Microbial Degradation of Natural and Anthropogenic Phosphonates.
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Review of phosphonate catabolism pathways distinguishing hydrolytic PhnWAY route from broad-spectrum C-P lyase. E. coli primarily uses the C-P lyase phnCDEFGHIJLKMNOP operon under Pho regulon control, while PhnA-type hydrolytic pathways are typically substrate-inducible and phosphate-independent in other organisms.
"Hydrolytic and oxidative phosphonate catabolic systems are often substrate-specific, whereas C-P lyase is broad-spectrum"
Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.
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DeepECTF predicted EC 3.11.1.2 for YjdM with low confidence (CS=1)
"the PhnA activity observed in vitro is not supported, and additional in vivo experiments are required to confirm the biological role of this enzyme. This prediction was given a CS of 1."
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The true PhnA family is nonhomologous to YjdM
"The experimentally validated PhnA is part of a nonhomologous family"
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Expression of PhnA family members in E. coli suggested PhnA activity was not present
"expression of members of this family in E. coli suggested that PhnA activity was not present in this organism (Kulakova et al. 1997)"
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Initial yjdM-phosphonate link refuted by Metcalf and Wanner 1993
"Underscoring the challenges in annotations, the initial report that the protein was involved in phosphonate catabolism was later refuted with additional genetic analyses (Metcalf and Wanner 1993)"
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Genome neighborhoods show yjdM not near phosphonate genes outside E. coli
"except for E. coli, yjdM genes are generally not close to phosphonate catabolism or transport genes"
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Classic case of in vitro activity not equaling in vivo function
"the PhnA activity observed in vitro is not supported, and additional in vivo experiments are required to confirm the biological role of this enzyme"