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 : cdpea_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YPL061W YDR035W YGR087C YLR044C YLR134W YDR380W YDL080C YMR009W YKL192C YPL148C YCL025C YKR039W YOL020W YOL059W YIL053W YER062C YGR191W YJR078W YJL121C YLR348C YPL092W YML120C YDR402C YFR047C YOR155C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.104748 (mmol/gDw/h)
  Minimum Production Rate : 0.006665 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.422512
  EX_pi_e : 0.046044
  EX_so4_e : 0.008097

Product: (mmol/gDw/h)
  EX_h_e : 23.081214
  EX_h2o_e : 13.335842
  EX_succ_e : 7.234548
  EX_3c3hmp_e : 3.634184
  EX_gly_e : 0.350814
  EX_etoh_e : 0.243068
  EX_xan_e : 0.105243
  Auxiliary production reaction : 0.006666
  EX_pap_e : 0.006002
  EX_hxan_e : 0.001959
  EX_for_e : 0.000542

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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