Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks (Q28084922)

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John A Gerlt

1

object named as

John A. Gerlt

1 reference

Jason T. Bouvier

2

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Daniel B. Davidson

3

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David R. Slater

6

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Katie L. Whalen

7

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language of work or name

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August 2015

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Biochimica et Biophysica Acta

published in

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volume

1854

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issue

8

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page(s)

1019-37

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describes a project that uses

Cytoscape

1 reference

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

cites work

The InterPro protein families database: the classification resource after 15 years

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Enzymatic and structural characterization of rTSγ provides insights into the function of rTSβ

20 March 2017

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A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization

20 March 2017

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Prospecting for Unannotated Enzymes: Discovery of a 3′,5′-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily

20 March 2017

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Discovery of new enzymes and metabolic pathways by using structure and genome context

20 March 2017

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Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily

20 March 2017

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Structural and Mechanistic Characterization of l -Histidinol Phosphate Phosphatase from the Polymerase and Histidinol Phosphatase Family of Proteins

20 March 2017

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The Enzyme Function Initiative

20 March 2017

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Structure and Function of YghU, a Nu-Class Glutathione Transferase Related to YfcG from Escherichia coli

20 March 2017

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Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

20 March 2017

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Formation and stability of a vinyl carbanion at the active site of orotidine 5'-monophosphate decarboxylase: pKa of the C-6 proton of enzyme-bound UMP

20 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Prediction and assignment of function for a divergent N-succinyl amino acid racemase

20 March 2017

1 reference

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Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons

20 March 2017

1 reference

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Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

20 March 2017

1 reference

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Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup

20 March 2017

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Structure-guided discovery of new deaminase enzymes

20 March 2017

1 reference

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Pfam: the protein families database

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

UniProt: a hub for protein information

20 March 2017

1 reference

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

7 April 2017

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Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

7 April 2017

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Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB.

29 September 2017

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Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily.

29 September 2017

1 reference

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Prediction of substrates for glutathione transferases by covalent docking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere

29 September 2017

1 reference

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The Structure-Function Linkage Database

29 September 2017

1 reference

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Discovery of a cAMP deaminase that quenches cyclic AMP-dependent regulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Consequences of domain insertion on sequence-structure divergence in a superfold

29 September 2017

1 reference

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Discovery of an L-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Pythoscape: a framework for generation of large protein similarity networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Divergent evolution in enolase superfamily: strategies for assigning functions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Inference of functional properties from large-scale analysis of enzyme superfamilies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

The evolution of function in strictosidine synthase-like proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Discovery of a cytokinin deaminase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

A novel operon encoding formaldehyde fixation: the ribulose monophosphate pathway in the gram-positive facultative methylotrophic bacterium Mycobacterium gastri MB19

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

A Unique cis-3-Hydroxy-l-proline Dehydratase in the Enolase Superfamily

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Predicting substrates by docking high-energy intermediates to enzyme structures

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?

27 November 2018

1 reference