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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2779 b3617 b2407 b1779 b1982 b0675 b2361 b0261 b2913 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448163 (mmol/gDw/h)
  Minimum Production Rate : 1.456871 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.064035
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.754368
  EX_pi_e : 1.889172
  EX_so4_e : 0.112856
  EX_k_e : 0.087478
  EX_fe2_e : 0.007198
  EX_mg2_e : 0.003888
  EX_ca2_e : 0.002333
  EX_cl_e : 0.002333
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.959878
  EX_co2_e : 24.839769
  EX_h_e : 7.032797
  EX_acald_e : 2.553885
  Auxiliary production reaction : 1.456871
  DM_oxam_c : 0.000501
  DM_5drib_c : 0.000301
  EX_glyc__R_e : 0.000150
  DM_4crsol_c : 0.000100

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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