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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b4069 b1479 b0910 b2297 b2458 b2779 b3617 b3236 b2463 b3962 b0104 b2210 b4267 b1033 b0675 b3551 b1014 b0822 b2799 b2913 b4219 b1832 b1778 b0452 b2975 b0114 b3603 b0306 b1539 b3605 b2492 b0904 b1380 b1710 b2480 b4266 b1206 b0221 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463013 (mmol/gDw/h)
  Minimum Production Rate : 0.081625 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.682131
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.000503
  EX_pi_e : 0.446625
  EX_so4_e : 0.116596
  EX_k_e : 0.090377
  EX_mg2_e : 0.004017
  EX_fe2_e : 0.003821
  EX_fe3_e : 0.003615
  EX_ca2_e : 0.002410
  EX_cl_e : 0.002410
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.896126
  EX_co2_e : 38.589412
  EX_h_e : 5.460900
  EX_ac_e : 1.039531
  Auxiliary production reaction : 0.081625
  EX_glyc__R_e : 0.000155
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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