(Q33790522)

29 July 2017

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes (English)

1 reference

29 July 2017

Kazuharu Arakawa

2

0 references

author name string

Nobuaki Kono

series ordinal

1

1 reference

29 July 2017

Masaru Tomita

series ordinal

3

1 reference

29 July 2017

language of work or name

English

0 references

publication date

11 January 2011

1 reference

29 July 2017

1 reference

29 July 2017

12

1 reference

29 July 2017

19

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-12-19

29 July 2017

0 references

cites work

Hidden Markov model speed heuristic and iterative HMM search procedure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Are two better than one? Analysis of an FtsK/Xer recombination system that uses a single recombinase

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Molecular keys of the tropism of integration of the cholera toxin phage

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Fully efficient chromosome dimer resolution in Escherichia coli cells lacking the integral membrane domain of FtsK.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

KEGG for representation and analysis of molecular networks involving diseases and drugs

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

VEJ{phi}, a novel filamentous phage of Vibrio cholerae able to transduce the cholera toxin genes.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

The dif/Xer recombination systems in proteobacteria

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Asymmetric DNA requirements in Xer recombination activation by FtsK

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

The replication fork trap and termination of chromosome replication

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

FtsK-dependent dimer resolution on multiple chromosomes in the pathogen Vibrio cholerae

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

The unconventional Xer recombination machinery of Streptococci/Lactococci

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Analysis of the terminus region of the Caulobacter crescentus chromosome and identification of the dif site

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

The bifunctional FtsK protein mediates chromosome partitioning and cell division in Caulobacter

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Origin of replication in circular prokaryotic chromosomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

YASS: enhancing the sensitivity of DNA similarity search

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Genetic recombination and the cell cycle: what we have learned from chromosome dimers

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Smarter than the average phage.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Multiple pathways process stalled replication forks

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Asymmetric activation of Xer site-specific recombination by FtsK.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

VGJ phi, a novel filamentous phage of Vibrio cholerae, integrates into the same chromosomal site as CTX phi.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Bacterial chromosome dynamics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Species specificity in the activation of Xer recombination at dif by FtsK.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

oriC region and replication termination site, dif, of the Xanthomonas campestris pv. campestris 17 chromosome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

FtsK Is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Identification and characterization of the dif Site from Bacillus subtilis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

FtsK functions in the processing of a Holliday junction intermediate during bacterial chromosome segregation.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

A greedy algorithm for aligning DNA sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Hidden Markov models for detecting remote protein homologies

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Profile hidden Markov models

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Analyzing genomes with cumulative skew diagrams

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Characterization of DinR, the Bacillus subtilis SOS repressor

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Asymmetric substitution patterns in the two DNA strands of bacteria

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Interactions of the site-specific recombinases XerC and XerD with the recombination site dif.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Inhibition of replication forks exiting the terminus region of the Escherichia coli chromosome occurs at two loci separated by 5 min.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

The terminus region of the Escherichia coli chromosome contains two separate loci that exhibit polar inhibition of replication

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Evidence of a ter specific binding protein essential for the termination reaction of DNA replication in Escherichia coli

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Site-specific recombination promoted by a short DNA segment of plasmid R1 and by a homologous segment in the terminus region of the Escherichia coli chromosome.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

Evidence for a fixed termination site of chromosome replication in Escherichia coli K12

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025954

4 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

The cytoplasmic domain of FtsK protein is required for resolution of chromosome dimers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

FtsK activities in Xer recombination, DNA mobilization and cell division involve overlapping and separate domains of the protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Delayed activation of Xer recombination at dif by FtsK during septum assembly in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Oriented loading of FtsK on KOPS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Dissection of a functional interaction between the DNA translocase, FtsK, and the XerD recombinase

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Characterization of XerC- and XerD-dependent CTX phage integration in Vibrio cholerae

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Termination structures in the Escherichia coli chromosome replication fork trap

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Recombinase binding specificity at the chromosome dimer resolution site dif of Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Noise-reduction filtering for accurate detection of replication termini in bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Filamentous phage integration requires the host recombinases XerC and XerD

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-19

Restriction of the activity of the recombination site dif to a small zone of the Escherichia coli chromosome

21 January 2018

1 reference

12 December 2020

Plasmids carrying cloned fragments of RF DNA from the filamentous phage (phi)Lf can be integrated into the host chromosome via site-specific integration and homologous recombination

1 reference

12 December 2020

The Single-Stranded Genome of Phage CTX Is the Form Used for Integration into the Genome of Vibrio cholerae

1 reference

12 December 2020

Chromosomal constraints in Gram-positive bacteria revealed by artificial inversions

1 reference

12 December 2020

Site-specific recombination at dif by Haemophilus influenzae XerC

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2164-12-19

1 reference

Dimensions Publication ID

29 July 2017

0 references

1 reference

29 July 2017

1 reference