Obtain proteomes
SEEK ID: https://ibisbahub.eu/assays/28
Experimental assay
Projects: An inventory of the Aspergillus niger secretome by combining in silico p...
Investigation: In-silico prediction and mass spectrometric validation of the Aspergillus niger secretome
Study: In-Silico Prediction
Assay position:
Assay type: Comparative Genomics
Technology type: Next generation sequencing
Organisms: No organisms
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Created: 18th May 2020 at 16:02
Last updated: 18th May 2020 at 16:02
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Projects: Uncurated Protocols Library, FLOX: FLavin-containing OXidoreductases, PlanOvac, HIGHFLUX, SporeDel, Yeast Glycerol, Galambr, SULFOCEL, An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, Template library, Muconic Acid Production in Yeast, IBISBA 1.0 deliverables, PREP-IBISBA deliverables, Biocare, test, DBTL-P, Upscale of the biocatalytic transformation of Free Fatty Acids into high-value products (BIOFFA), B-PAC, BIOFFA, GLYCOMICS, KorallionBio, MAROX, PROTEIFROM, SUPI, Bioindustry4.0 Work Package 7: Tools for high-quality datasets, requisite for data-driven methods and services
Institutions: UNIMAN - The University of Manchester, UAB - Universitat Autònoma de Barcelona, CNR - Consiglio Nazionale delle Ricerche, INSAT - Institut National des Science Appliquees de Toulouse, VTT - Teknologian tutkimuskeskus VTT Oy, VITO - Vlaamse Instelling voor Technologisch Onderzoek N.V.
Files and projects to support the IBISBA 2020 f2f
Projects: An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, Example testing project
Web page: Not specified
The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N- terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current ...
Programme: IBISBA 2020 f2f
Public web page: Not specified
Start date: 1st Jul 2019
End date: 31st Dec 2019
Submitter: Munazah Andrabi
Studies: Culture experiments, In-Silico Prediction, Metabolic model analysis, Validation of the secretome of Aspergillus niger
Assays: GPI Anchor Predictions, Growth experiment, Identify enzymes from spectra, Liquid chromatography tandem mass spectrometry, Mass Spectrometry Analysis, Obtain metabolic model, Obtain proteomes, Orthology identification, Signal Peptide Predictions
A majority rule based classifier that evaluates signal peptide (SP) predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome.
Submitter: Munazah Andrabi
Investigation: In-silico prediction and mass spectrometric val...
Assays: GPI Anchor Predictions, Obtain proteomes, Orthology identification, Signal Peptide Predictions
