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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (1 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b1478 b1241 b4069 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2799 b3945 b1602 b0153 b4381 b0584 b0529 b2492 b0904 b1380 b2660 b1511 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443666 (mmol/gDw/h)
  Minimum Production Rate : 0.522523 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.835990
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.540026
  EX_pi_e : 0.950486
  EX_so4_e : 0.111724
  EX_k_e : 0.086600
  EX_fe2_e : 0.007126
  EX_mg2_e : 0.003849
  EX_ca2_e : 0.002309
  EX_cl_e : 0.002309
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.601298
  EX_co2_e : 35.951246
  EX_h_e : 6.083348
  Auxiliary production reaction : 0.522523
  EX_hxan_e : 0.437119
  EX_ac_e : 0.258296
  DM_mththf_c : 0.000199
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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