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 : urdglyc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b0469 b0238 b0125 b3831 b4069 b4384 b3926 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b0477 b4139 b2498 b0505 b1602 b0511 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.501756 (mmol/gDw/h)
  Minimum Production Rate : 0.296364 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.453005
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.013343
  EX_pi_e : 0.483997
  EX_so4_e : 0.126352
  EX_k_e : 0.097939
  EX_fe2_e : 0.008059
  EX_mg2_e : 0.004353
  EX_ca2_e : 0.002612
  EX_cl_e : 0.002612
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.072661
  EX_co2_e : 37.930192
  EX_h_e : 5.793234
  Auxiliary production reaction : 0.296364
  EX_ac_e : 0.292116
  EX_ade_e : 0.000338
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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