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Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks
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Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks
(English)
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author
Boris Sadkhin
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Boris Sadkhin
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5
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Heidi J. Imker
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Heidi J. Imker
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4
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John A Gerlt
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John A. Gerlt
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Jason T. Bouvier
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2
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Daniel B. Davidson
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3
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David R. Slater
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6
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Katie L. Whalen
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7
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English
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publication date
August 2015
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published in
Biochimica et Biophysica Acta
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volume
1854
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PubMed
issue
8
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PubMed
page(s)
1019-37
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PubMed
describes a project that uses
Cytoscape
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Europe PubMed Central
retrieved
9 June 2022
reference URL
https://europepmc.org/search?query=(METHODS:'Cytoscape')
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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
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20 March 2017
A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization
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20 March 2017
Prospecting for Unannotated Enzymes: Discovery of a 3′,5′-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily
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20 March 2017
Discovery of new enzymes and metabolic pathways by using structure and genome context
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20 March 2017
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily
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20 March 2017
Structural and Mechanistic Characterization of l -Histidinol Phosphate Phosphatase from the Polymerase and Histidinol Phosphatase Family of Proteins
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20 March 2017
The Enzyme Function Initiative
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PubMed Central
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20 March 2017
Structure and Function of YghU, a Nu-Class Glutathione Transferase Related to YfcG from Escherichia coli
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20 March 2017
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
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20 March 2017
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
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20 March 2017
Prediction and assignment of function for a divergent N-succinyl amino acid racemase
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20 March 2017
Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase
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PubMed Central
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20 March 2017
Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons
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20 March 2017
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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20 March 2017
Structure-guided discovery of new deaminase enzymes
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20 March 2017
Pfam: the protein families database
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20 March 2017
UniProt: a hub for protein information
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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7 April 2017
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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7 April 2017
Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
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PubMed Central
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29 September 2017
Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB.
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29 September 2017
Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach
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PubMed Central
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29 September 2017
Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution
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29 September 2017
Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism
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PubMed Central
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29 September 2017
Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis
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29 September 2017
Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily.
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29 September 2017
Prediction of substrates for glutathione transferases by covalent docking
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29 September 2017
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere
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29 September 2017
The Structure-Function Linkage Database
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PubMed Central
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PubMed Central
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Consequences of domain insertion on sequence-structure divergence in a superfold
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PubMed Central
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29 September 2017
Discovery of an L-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily
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PubMed Central
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29 September 2017
Pythoscape: a framework for generation of large protein similarity networks
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29 September 2017
Divergent evolution in enolase superfamily: strategies for assigning functions
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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29 September 2017
Inference of functional properties from large-scale analysis of enzyme superfamilies
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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The evolution of function in strictosidine synthase-like proteins
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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Discovery of a cytokinin deaminase
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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29 September 2017
Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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29 September 2017
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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29 September 2017
Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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A novel operon encoding formaldehyde fixation: the ribulose monophosphate pathway in the gram-positive facultative methylotrophic bacterium Mycobacterium gastri MB19
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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2 June 2018
The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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A Unique cis-3-Hydroxy-l-proline Dehydratase in the Enolase Superfamily
1 reference
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PubMed Central
reference URL
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27 November 2018
GenBank
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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27 November 2018
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
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27 November 2018
Predicting substrates by docking high-energy intermediates to enzyme structures
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
retrieved
27 November 2018
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.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
retrieved
27 November 2018
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
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
retrieved
27 November 2018
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
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
retrieved
27 November 2018
How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4457552
retrieved
27 November 2018
Identifiers
DOI
10.1016/J.BBAPAP.2015.04.015
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3566757
OpenCitations bibliographic resource ID
3566757
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3566757
PMC publication ID
4457552
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3566757
PubMed publication ID
25900361
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3566757
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