(Q35364992)

8 August 2017

title

Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence (English)

1 reference

8 August 2017

0 references

1 reference

whole genome sequencing

1 reference

Hiroshi Mori

5

0 references

Manabu Fukui

10

object named as

Manabu Fukui

1 reference

8 August 2017

Hisaya Kojima

1

1 reference

8 August 2017

Yoshitoshi Ogura

2

1 reference

8 August 2017

Nozomi Yamamoto

3

1 reference

8 August 2017

Tomoaki Togashi

4

1 reference

8 August 2017

Tomohiro Watanabe

6

1 reference

8 August 2017

Fumiko Nemoto

7

1 reference

8 August 2017

Ken Kurokawa

8

1 reference

8 August 2017

Tetsuya Hayashi

9

1 reference

8 August 2017

publication date

24 October 2014

1 reference

8 August 2017

1 reference

8 August 2017

volume

9

1 reference

8 August 2017

issue

5

1 reference

8 August 2017

page(s)

1166-1176

1 reference

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

8 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Data, information, knowledge and principle: back to metabolism in KEGG

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Phylogenetic and morphologic complexity of giant sulphur bacteria.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Mobile elements in a single-filament orange Guaymas Basin Beggiatoa ("Candidatus Maribeggiatoa") sp. draft genome: evidence for genetic exchange with cyanobacteria

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

The bacterial SoxAX cytochromes.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Unusual polyphosphate inclusions observed in a marine Beggiatoa strain.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Fast and accurate short read alignment with Burrows-Wheeler transform

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Methylotrophy in freshwater Beggiatoa alba strains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Insights into the genome of large sulfur bacteria revealed by analysis of single filaments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

High Nitrate Concentrations in Vacuolate, Autotrophic Marine Beggiatoa spp.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Morphological and phylogenetic characterizations of freshwater Thioploca species from Lake Biwa, Japan, and Lake Constance, Germany

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Ecology of Thioploca spp.: nitrate and sulfur storage in relation to chemical microgradients and influence of Thioploca spp. on the sedimentary nitrogen cycle.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Adaptation of Escherichia coli to high osmolarity environments: osmoregulation of the high-affinity glycine betaine transport system proU.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Close association of active nitrifiers with Beggiatoa mats covering deep-sea hydrothermal sediments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Vacuolar respiration of nitrate coupled to energy conservation in filamentous Beggiatoaceae.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Colorless sulfur bacteria Thioploca from different sites in Lake Baikal

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Prediction of effective genome size in metagenomic samples

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Community structure of bacteria associated with sheaths of freshwater and brackish thioploca species

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Molecular basis of intramolecular electron transfer in sulfite-oxidizing enzymes is revealed by high resolution structure of a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409161

Description of Thioploca ingrica sp. nov., nom. rev.

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FISMEJ.2014.209

Large Sulfur Bacteria and the Formation of Phosphorite

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FISMEJ.2014.209

Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FISMEJ.2014.209

The fine structure of Thioploca ingrica and a comparison with Beggiatoa

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25343513

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Diversity of freshwater Thioploca species and their specific association with filamentous bacteria of the phylum Chloroflexi

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25343513

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Carbon source utilization and accumulation of respiration-related substances by freshwater Thioploca species

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25343513

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/ISMEJ.2014.209

1 reference

8 August 2017

1 reference

8 August 2017

1 reference