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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b0871 b2779 b2925 b2097 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b0937 b1982 b2799 b3945 b1602 b2406 b1727 b0529 b2492 b0904 b3927 b1380 b2660 b3662 b1518 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467530 (mmol/gDw/h)
  Minimum Production Rate : 0.018183 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.674138
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.141451
  EX_pi_e : 0.487347
  EX_so4_e : 0.117733
  EX_k_e : 0.091258
  EX_fe2_e : 0.007509
  EX_mg2_e : 0.004056
  EX_ca2_e : 0.002433
  EX_cl_e : 0.002433
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.210982
  EX_co2_e : 40.625612
  EX_h_e : 4.369837
  Auxiliary production reaction : 0.018183
  EX_hxan_e : 0.000315
  DM_mththf_c : 0.000209
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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