Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: metagenomic amplicon sequencing of NRPS and PKS domains along environmental gradients

PROVIDER: PRJNA828401 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18829000_1.fastq.gz	Fastqsanger.gz
	SRR18829000_2.fastq.gz	Fastqsanger.gz
	SRR18832600_1.fastq.gz	Fastqsanger.gz
	SRR18832600_2.fastq.gz	Fastqsanger.gz
	SRR18837000_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 792

Similar Datasets

Project description:metagenomic amplicon sequencing of NRPS domains in permafrost soils

| PRJNA976646 | ENA

Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan

Project description:Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides biosynthesized by animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional enzymes expressed in the CANs that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes and discover a mechanism for trafficking intermediates between a PKS and an NRPS. Specifically, the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking mechanism provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis.

2021-06-22 | MTBLS2313 | MetaboLights

Exploring the selectivity and engineering potential of an NRPS condensation domain involved in the biosynthesis of the thermophilic siderophore fuscachelin

Project description:Condensation (C) domains are the key component linking different monomers together, typically forming peptide bonds and occasionally ester bonds, during the nonribosomal peptide synthetase (NRPS). While A domains have been well characterised due to their role in selectivity of the monomers and functioning as a gate keeper in the NRPS biosynthesis, C domains have been a subject of debate as they have not demonstrated signs of “A-domain like” side chain selectivity of its acceptor side. Here, we report our biochemical and structural characterisation of the selectivity of the fuscachelin C3-domain showing that it is not broadly flexible for monomers at the acceptor site, suggesting the need to consider C-domain mutation regarding future NRPS engineering.

2023-06-02 | PXD040334 | Pride

Project description:Linking bacterial community composition to water salinity along environmental gradients

| PRJNA600834 | ENA

undefined

Project description:18S V4 amplicon sequencing of soil DNA samples collected along environmental gradients in a forest area in southern Norway

| PRJEB55259 | ENA

Sulfate reducing bacteria associated to diatoms during a spring phytoplankton bloom

Project description:Phytoplankton blooms represent hotspots of primary production and lead to the formation of particulate organic matter composed of living and dead algal cells. These particles are characterized by steep chemical gradients, for instance in oxygen concentration, that provide diverse ecological niches for specifically adapted microbes to thrive. Particulate fractions were collected at almost daily intervals between early March and late May in 2018. Amplicon sequencing and Meta-omics was used to asses microbial community composition and functionality at different time points.

2024-04-02 | PXD035982 | Pride

Project description:Microbial diversity and analysis of PKS and NRPS in the marine sponge Callyspongiya diffusa using whole metagenomic approach

| PRJNA662333 | ENA

Project description:Fine-scale trait variation of five native forbs along environmental gradients

| PRJNA983821 | ENA

NRPS X-Link (Alb02) from Albicidin

Project description:Bottom-up proteomics (trypsin DDA Top5) of crosslinked ALb02 and NRPS T-domains.

2020-06-03 | MSV000085542 | MassIVE

LC-MS/MS of autotrophic culture KS, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.

2021-05-17 | PXD023186 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data