MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b3708 b2297 b2458 b2926 b3617 b0030 b2407 b3236 b2883 b2797 b3117 b1814 b4471 b2210 b4381 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.570196 (mmol/gDw/h)
  Minimum Production Rate : 0.559056 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.372914
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.029868
  EX_pi_e : 1.668127
  EX_so4_e : 0.143587
  EX_k_e : 0.111298
  EX_fe2_e : 0.009158
  EX_mg2_e : 0.004946
  EX_ca2_e : 0.002968
  EX_cl_e : 0.002968
  EX_cu2_e : 0.000404
  EX_mn2_e : 0.000394
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.631893
  EX_co2_e : 27.153826
  EX_h_e : 9.438875
  EX_ac_e : 1.886943
  Auxiliary production reaction : 0.559056
  EX_ade_e : 0.015303
  DM_mththf_c : 0.000255
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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.

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Last updated: 21-Sep-2023
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