(Q28974902)

21 March 2017

title

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours (English)

1 reference

21 March 2017

1 reference

10

0 references

Jean Weissenbach

9

0 references

Marcel Salanoubat

7

0 references

Kiran R Patil

Kiran R. Patil

8

0 references

Jeroen Raes

Jeroen Raes

3

0 references

Aleksej Zelezniak

Aleksej Zelezniak

4

0 references

Nadia Perchat

5

Nadia Perchat

1 reference

21 March 2017

Takuji Yamada

1

1 reference

21 March 2017

Alison S. Waller

2

1 reference

21 March 2017

Alain Perret

6

1 reference

21 March 2017

publication date

8 May 2012

1 reference

Molecular Systems Biology

21 March 2017

published in

1 reference

21 March 2017

volume

8

1 reference

21 March 2017

page(s)

581

1 reference

SMART 7: recent updates to the protein domain annotation resource

21 March 2017

cites work

1 reference

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Enterotypes of the human gut microbiome

23 March 2017

1 reference

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Environments that induce synthetic microbial ecosystems

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

SmashCommunity: a metagenomic annotation and analysis tool

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

High-throughput generation, optimization and analysis of genome-scale metabolic models

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

A human gut microbial gene catalogue established by metagenomic sequencing

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

The genetic landscape of a cell

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

The Pfam protein families database

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

KEGG for linking genomes to life and the environment

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

STRING 7--recent developments in the integration and prediction of protein interactions

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Metagenomic analysis of the human distal gut microbiome

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Environmental genome shotgun sequencing of the Sargasso Sea

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

An efficient algorithm for large-scale detection of protein families

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Applications of genome-scale metabolic reconstructions

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

6 April 2017

2 references

https://api.crossref.org/works/10.1038/MSB.2012.13

22 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Community structure and metabolism through reconstruction of microbial genomes from the environment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

A new generation of homology search tools based on probabilistic inference

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Protein interaction maps for complete genomes based on gene fusion events

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Conservation of gene order: a fingerprint of proteins that physically interact

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Quantitative assessment of protein function prediction from metagenomics shotgun sequences

7 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2012.13

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Molecular basis for mycophenolic acid biosynthesis in Penicillium brevicompactum

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Identification of essential genes in C. jejuni genome highlights hyper-variable plasticity regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Phenotypic landscape of a bacterial cell

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Protein promiscuity and its implications for biotechnology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Cell and molecular aspects of human intestinal biotin absorption

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

C-terminal residues of mature human T-lymphotropic virus type 1 protease are critical for dimerization and catalytic activity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Construction of consecutive deletions of the Escherichia coli chromosome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

A survey of orphan enzyme activities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Identifying metabolic enzymes with multiple types of association evidence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Extraction of phylogenetic network modules from the metabolic network

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Flux coupling analysis of genome-scale metabolic network reconstructions.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Missing genes in metabolic pathways: a comparative genomics approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Function prediction and protein networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Comparative analysis of regulatory patterns in bacterial genomes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

The purification and properties of l-histidine-2-oxoglutarate aminotransferase from Pseudomonas testosteroni

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Asparagine transaminase from rat liver

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377989

Predicting genes for orphan metabolic activities using phylogenetic profiles

3 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2012.13

Introduction of a (poly)histidine tag in L-lactate dehydrogenase produces a mixture of active and inactive molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2012.13

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/22569339

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Preparative synthesis of GDP-beta-L-fucose by recombinant enzymes from enterobacterial sources

1 reference

https://pubmed.ncbi.nlm.nih.gov/22569339

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/MSB.2012.13

1 reference

1 reference

1 reference

1 reference