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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b1241 b0351 b3831 b4069 b3614 b0910 b4152 b2297 b2458 b2926 b3617 b0030 b1238 b1612 b1611 b4122 b0651 b2162 b3962 b4267 b2799 b4138 b4123 b0621 b4381 b2406 b2868 b0114 b0509 b3125 b0529 b1539 b2492 b0904 b4266 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.355190 (mmol/gDw/h)
  Minimum Production Rate : 0.072398 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.659882
  EX_o2_e : 282.350821
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.689357
  EX_pi_e : 0.342618
  EX_so4_e : 0.089444
  EX_k_e : 0.069331
  EX_mg2_e : 0.003081
  EX_ca2_e : 0.001849
  EX_cl_e : 0.001849
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994295
  EX_h2o_e : 549.496850
  EX_co2_e : 31.820008
  EX_succ_e : 0.761985
  EX_ac_e : 0.693481
  EX_ura_e : 0.643478
  EX_xan_e : 0.391595
  DM_mththf_c : 0.217354
  Auxiliary production reaction : 0.072398
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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