MetNetComp

MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iMM904 [2].
Target metabolite : pendp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 52: See next) for growth-coupled production (at least stoichioemetrically feasible)
Gene deletion size : 26
Gene deletion: YHR104W YBR068C YDR046C YBR069C YGR087C YLR044C YLR134W YDR380W YDL080C YDR508C YCL025C YKR039W YIL053W YER062C YDR300C YDL171C YLR348C YKL085W YCL064C YLR164W YDR178W YDL085W YMR145C YEL046C YKL218C YKL184W (List of alternative genes)
Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
Growth Rate : 0.112513 (mmol/gDw/h)
Minimum Production Rate : 0.014551 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
EX_glc__D_e : 9.207297
EX_nh4_e : 2.360356
EX_o2_e : 2.000000
EX_pi_e : 0.054278
EX_so4_e : 0.008697

Product: (mmol/gDw/h)
EX_h_e : 21.624338
EX_h2o_e : 12.841151
EX_succ_e : 7.942090
EX_4abut_e : 1.730683
EX_3c3hmp_e : 1.729761
Auxiliary production reaction : 0.016017

Visualization
1. Download JSON file.
2. Go to Escher site [3].
3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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