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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b4382 b4069 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b2297 b2458 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0595 b0261 b3945 b0507 b2406 b0112 b2943 b0114 b2366 b0529 b2492 b0904 b2947 b2578 b1533 b3927 b3825 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.689092 (mmol/gDw/h)
  Minimum Production Rate : 0.138358 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.301955
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.733677
  EX_pi_e : 0.941419
  EX_so4_e : 0.173527
  EX_k_e : 0.134506
  EX_fe2_e : 0.011068
  EX_mg2_e : 0.005978
  EX_ca2_e : 0.003587
  EX_cl_e : 0.003587
  EX_cu2_e : 0.000489
  EX_mn2_e : 0.000476
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 48.279769
  EX_co2_e : 25.471567
  EX_h_e : 7.748428
  EX_ac_e : 0.401180
  EX_trp__L_e : 0.230309
  Auxiliary production reaction : 0.138358
  DM_oxam_c : 0.000771
  DM_5drib_c : 0.000462
  DM_4crsol_c : 0.000154

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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