Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. (Q34787593)

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English	Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA.	scientific article

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scholarly article

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Europe PubMed Central

PubMed publication ID

4 August 2017

Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. (English)

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

1 reference

based on heuristic

inferred from title

computational biology

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based on heuristic

inferred from title

Maxwell Burroughs

3

object named as

A Maxwell Burroughs

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Lakshminarayan M. Iyer

1

object named as

Lakshminarayan M Iyer

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

4

object named as

L Aravind

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object named as

Dapeng Zhang

2

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A Maxwell Burroughs

3

object named as

A Maxwell Burroughs

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

language of work or name

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publication date

28 June 2013

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Europe PubMed Central

PubMed publication ID

4 August 2017

Nucleic Acids Research

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Europe PubMed Central

PubMed publication ID

4 August 2017

41

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

16

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

7635-7655

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor

1 reference

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8 July 2018

TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS

1 reference

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8 July 2018

Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells

1 reference

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8 July 2018

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

1 reference

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8 July 2018

Genome-wide association meta-analysis identifies new endometriosis risk loci

1 reference

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8 July 2018

Retracted: GREB1 Functions as a Growth Promoter and Is Modulated by IL6/STAT3 in Breast Cancer

1 reference

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8 July 2018

Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing

1 reference

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8 July 2018

Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania

1 reference

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8 July 2018

Gene flow and biological conflict systems in the origin and evolution of eukaryotes

1 reference

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8 July 2018

Complete genome sequences of two Persicivirga bacteriophages, P12024S and P12024L

1 reference

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8 July 2018

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

1 reference

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8 July 2018

JBP1 and JBP2 proteins are Fe2+/2-oxoglutarate-dependent dioxygenases regulating hydroxylation of thymidine residues in trypanosome DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Swi2/Snf2 remodelers: hybrid views on hybrid molecular machines

1 reference

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8 July 2018

The secret lives of mycobacteriophages

1 reference

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8 July 2018

Biosynthesis of pyrrolopyrimidines

1 reference

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8 July 2018

Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL).

1 reference

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8 July 2018

The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications

1 reference

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8 July 2018

Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation

1 reference

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8 July 2018

The Pfam protein families database

1 reference

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8 July 2018

Chloroviruses: not your everyday plant virus

1 reference

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8 July 2018

Epigenetic Regulation of Polymerase II Transcription Initiation in Trypanosoma cruzi: Modulation of Nucleosome Abundance, Histone Modification, and Polymerase Occupancy by O-Linked Thymine DNA Glucosylation

1 reference

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8 July 2018

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems

1 reference

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8 July 2018

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Natural history of the eukaryotic chromatin protein methylation system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Natural history of eukaryotic DNA methylation systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Introduction--Epiphanies in epigenetics.

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8 July 2018

A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

1 reference

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8 July 2018

Twenty years hunting for sulfur in DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

FastTree 2--approximately maximum-likelihood trees for large alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

A new generation of homology search tools based on probabilistic inference

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Discovery and characterization of tRNAIle lysidine synthetase (TilS).

1 reference

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8 July 2018

Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2

1 reference

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8 July 2018

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

The structural and biochemical foundations of thiamin biosynthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Structural genomics reveals EVE as a new ASCH/PUA-related domain

1 reference

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8 July 2018

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Searching protein structure databases with DaliLite v.3

1 reference

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8 July 2018

The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix

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8 July 2018

Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems

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8 July 2018

Base J: Discovery, Biosynthesis, and Possible Functions

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8 July 2018

Glycosyltransferases: structures, functions, and mechanisms

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8 July 2018

The Jpred 3 secondary structure prediction server

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8 July 2018

The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5'-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119.

1 reference

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8 July 2018

MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases

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8 July 2018

Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain

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8 July 2018

DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

The NYN domains: novel predicted RNAses with a PIN domain-like fold

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8 July 2018

The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

GREB1 is a novel androgen-regulated gene required for prostate cancer growth.

1 reference

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8 July 2018

Evolutionary genomics of nucleo-cytoplasmic large DNA viruses

1 reference

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8 July 2018

Homing endonuclease structure and function

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8 July 2018

The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

The HHpred interactive server for protein homology detection and structure prediction

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8 July 2018

Genomic analysis of bacteriophage PhiJL001: insights into its interaction with a sponge-associated alpha-proteobacterium

1 reference

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8 July 2018

Genome of bacteriophage P1

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8 July 2018

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

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8 July 2018

Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages

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8 July 2018

Legionella drancourtii sp. nov., a strictly intracellular amoebal pathogen

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8 July 2018

Evolution and classification of P-loop kinases and related proteins

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8 July 2018

An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.

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8 July 2018

The natural occurrence of ethionine in bactdria

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8 July 2018

Three monophyletic superfamilies account for the majority of the known glycosyltransferases

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8 July 2018

Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme

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8 July 2018

Activation of prophage eib genes for immunoglobulin-binding proteins by genes from the IbrAB genetic island of Escherichia coli ECOR-9.

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8 July 2018

An alternative flavin-dependent mechanism for thymidylate synthesis

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8 July 2018

Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.

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8 July 2018

The GTP-dependent restriction enzyme McrBC from Escherichia coli forms high-molecular mass complexes with DNA and produces a cleavage pattern with a characteristic 10-base pair repeat.

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8 July 2018

Comparative genomics and evolution of proteins involved in RNA metabolism

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8 July 2018

The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates

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8 July 2018

PDZK1 and GREB1 are estrogen-regulated genes expressed in hormone-responsive breast cancer.

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8 July 2018

A viral member of the ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation

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8 July 2018

The DNA methyltransferases of mammals

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8 July 2018

DNA bending and a flip-out mechanism for base excision by the helix–hairpin–helix DNA glycosylase, Escherichia coli AlkA

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8 July 2018

Plasmid RK2 ParB protein: purification and nuclease properties.

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8 July 2018

Novel predicted RNA-binding domains associated with the translation machinery

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8 July 2018

The use of gene clusters to infer functional coupling

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8 July 2018

Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex

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8 July 2018

Conserved domains in DNA repair proteins and evolution of repair systems

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8 July 2018

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

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8 July 2018

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

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8 July 2018

GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Aminotransferases: demonstration of homology and division into evolutionary subgroups.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Biology of DNA restriction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Evidence of two levels of control of P1 oriR and host oriC replication origins by DNA adenine methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Hypermodified bases in DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

5-[(Hydroxymethyl)-O-pyrophosphoryl]uracil, an intermediate in the biosynthesis of alpha-putrescinylthymine in deoxyribonucleic acid of bacteriophage phi W-14.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Modified bases in bacteriophage DNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Synthesis of deoxythymidylate and the unusual deoxynucleotide in mature DNA of Bacillus subtilis bacteriophage SP10 occurs by postreplicational modification of 5-hydroxymethyldeoxyuridylate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Specificity of the bacteriophage Mu mom+ -controlled DNA modification.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Purification and characterization of the unusual deoxynucleoside, alpha-N-(9-beta-D-2'-deoxyribofuranosylpurin-6-yl)glycinamide, specified by the phage Mu modification function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Studies on the biosynthesis of alpha-putrescinylthymine in bacteriophage phi W-14-infected Pseudomonas acidovorans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Polymer-level synthesis of oxopyrimidine deoxynucleotides by Bacillus subtilis phage SP10: characterization of modification-defective mutants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Bacteriophage P1 cre gene and its regulatory region. Evidence for multiple promoters and for regulation by DNA methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

P1 plasmid replication requires methylated DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

8 July 2018

Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

26 October 2018

AglF, aglG and aglI, novel members of a gene island involved in the N-glycosylation of the Haloferax volcanii S-layer glycoprotein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

26 October 2018

Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

26 October 2018

Thermotoga maritima MazG protein has both nucleoside triphosphate pyrophosphohydrolase and pyrophosphatase activities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

26 October 2018

The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

26 October 2018

A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763556

26 October 2018

Polyamine biosynthesis in Escherichia coli: construction of polyamine-deficient mutants

1 reference

https://pubmed.ncbi.nlm.nih.gov/23814188

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Genome ofBacillus subtilisPhage SP10: A Comparative Analysis with Phage SPO1

1 reference

https://pubmed.ncbi.nlm.nih.gov/23814188

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Properties and specificity of methionyl-tRNAfMet formyltransferase from Escherichia coli

1 reference

https://pubmed.ncbi.nlm.nih.gov/23814188

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKT573

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

release_po57xspytbbnlksmtnseo4o72y

1 reference

https://api.fatcat.wiki/v0/release/po57xspytbbnlksmtnseo4o72y

24 November 2022

based on heuristic

mapped directly with Wikidata item

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

ResearchGate publication ID

0 references

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