(Q36663972)

English

Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks.

scientific article published on January 2013

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23315382%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks (English)

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23315382%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

bacterial evolution

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inferred from title

3

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22 February 2020

author name string

Motomu Matsui

1

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22 February 2020

Masaru Tomita

2

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22 February 2020

publication date

1 January 2013

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22 February 2020

Genome Biology and Evolution

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22 February 2020

5

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22 February 2020

2

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22 February 2020

267-282

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Europe PubMed Central

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22 February 2020

describes a project that uses

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Europe PubMed Central

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based on heuristic

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Genomic analysis of a key innovation in an experimental Escherichia coli population

1 reference

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1 reference

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1 reference

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1 reference

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RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

1 reference

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1 reference

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SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale

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SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building

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Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes

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Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.

1 reference

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30 September 2017

Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli

1 reference

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30 September 2017

Identification and characterization of an archaeon-specific riboflavin kinase

1 reference

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30 September 2017

Transcription factor distribution in Escherichia coli: studies with FNR protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria

1 reference

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30 September 2017

Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles

1 reference

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30 September 2017

Spectral clustering of protein sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Identification of the CRP regulon using in vitro and in vivo transcriptional profiling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Adaptive evolution of transcription factor binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

The natural history of nitrogen fixation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

CcpA-dependent carbon catabolite repression in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Evolution of transcription factors and the gene regulatory network in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

A comparative genomics approach to prediction of new members of regulons

1 reference

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Carbon catabolite repression in bacteria

1 reference

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30 September 2017

A novel regulatory switch mediated by the FNR-like protein of Lactobacillus casei

1 reference

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

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30 September 2017

Genetic regulation of nitrogen fixation in rhizobia.

1 reference

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30 September 2017

Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene

1 reference

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Replication properties of pIM13, a naturally occurring plasmid found in Bacillus subtilis, and of its close relative pE5, a plasmid native to Staphylococcus aureus

1 reference

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30 September 2017

fixK, a gene homologous with fnr and crp from Escherichia coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

FNR and its role in oxygen-regulated gene expression in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

30 September 2017

Correlated evolution of transcription factors and their binding sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

28 June 2018

Evolution of transcriptional regulatory circuits in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

28 June 2018

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3590769

28 June 2018

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1 reference

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28 June 2018

YeiL, the third member of the CRP-FNR family in Escherichia coli

1 reference

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28 June 2018

Co-evolution of proteins with their interaction partners

1 reference

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28 June 2018

Two operons that encode FNR-like proteins in Lactococcus lactis

1 reference

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28 June 2018

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1 reference

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28 June 2018

Interconversion of the DNA-binding specificities of two related transcription regulators, CRP and FNR.

1 reference

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1 reference

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28 June 2018

Regulation of FNR dimerization by subunit charge repulsion.

1 reference

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20 September 2018

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1 reference

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20 September 2018

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1 reference

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1 reference

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1 reference

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20 September 2018

DNA binding and dimerization of the Fe-S-containing FNR protein from Escherichia coli are regulated by oxygen.

1 reference

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Molecular evolution of nitrogen fixation: the evolutionary history of the nifD, nifK, nifE, and nifN genes

1 reference

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12 December 2020

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Homology between CAP and Fnr, a regulator of anaerobic respiration in Escherichia coli

1 reference

https://pubmed.ncbi.nlm.nih.gov/23315382

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/GBE/EVT004

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23315382%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23315382%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23315382%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

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