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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b1054 b3553 b1478 b4382 b0238 b0125 b1241 b0351 b4069 b4384 b2297 b2458 b2926 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0477 b1033 b4015 b0261 b0411 b2799 b3945 b1602 b3915 b4064 b4464 b0529 b2492 b0904 b1380 b2660 b0606 b0221 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368122 (mmol/gDw/h)
  Minimum Production Rate : 0.642976 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.320033
  EX_o2_e : 285.701220
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.573665
  EX_pi_e : 0.998068
  EX_so4_e : 0.092700
  EX_k_e : 0.071855
  EX_mg2_e : 0.003193
  EX_ca2_e : 0.001916
  EX_cl_e : 0.001916
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994088
  EX_h2o_e : 552.246427
  EX_co2_e : 34.433363
  EX_ac_e : 1.693624
  Auxiliary production reaction : 0.642976
  EX_xan_e : 0.256005
  EX_ade_e : 0.000412
  DM_5drib_c : 0.000247
  DM_4crsol_c : 0.000082

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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