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 : damp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0871 b2779 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b0937 b2799 b3945 b1602 b4381 b2975 b3603 b0529 b2492 b0904 b1380 b2660 b0514 b1511 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.429841 (mmol/gDw/h)
  Minimum Production Rate : 0.479956 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.643769
  EX_o2_e : 285.348444
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.042023
  EX_pi_e : 0.894583
  EX_so4_e : 0.108243
  EX_k_e : 0.083902
  EX_mg2_e : 0.003729
  EX_ca2_e : 0.002237
  EX_cl_e : 0.002237
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993096
  EX_h2o_e : 552.864261
  EX_co2_e : 35.757336
  EX_acald_e : 0.899575
  Auxiliary production reaction : 0.479956
  DM_mththf_c : 0.000193
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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