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Background  Genome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of multi-omics measurement techniques in recent years, new methods that integrating multi-omics data into the GSMM show promising effects on the predicted results. It does not only improve the accuracy of phenotype prediction but also enhances the reliability of the model for simulating complex biochemical phenomena, which can promote theoretical breakthroughs for specific gene target identification or better understanding the cell metabolism on the system level.    Results  Based on the basic GSMM model iHL1210 of  Aspergillus niger , we integrated large-scale enzyme kinetics and proteomics data to establish a GSMM based on enzyme constraints, termed a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO). The results show that enzyme constraints effectively improve the model’s phenotype prediction ability, and extended the model’s potential to guide target gene identification through predicting metabolic phenotype changes of  A. niger  by simulating gene knockout. In addition, enzyme constraints significantly reduced the solution space of the model, i.e., flux variability over 40.10% metabolic reactions were significantly reduced. The new model showed also versatility in other aspects, like estimating large-scale    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$k_{{cat}}$$\end{document}    k   catvalues, predicting the differential expression of enzymes under different growth conditions.    Conclusions  This study shows that incorporating enzymes’ abundance information into GSMM is very effective for improving model performance with  A. niger . Enzyme-constrained model can be used as a powerful tool for predicting the metabolic phenotype of  A. niger  by incorporating proteome data. In the foreseeable future, with the fast development of measurement techniques, and more precise and rich proteomics quantitative data being obtained for  A. niger , the enzyme-constrained GSMM model will show greater application space on the system level.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12934-021-01614-2.

Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions