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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b3399 b4069 b2744 b2297 b2458 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b3915 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.419272 (mmol/gDw/h)
  Minimum Production Rate : 0.379189 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.751214
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.425929
  EX_pi_e : 0.783622
  EX_so4_e : 0.105581
  EX_k_e : 0.081839
  EX_fe3_e : 0.006734
  EX_mg2_e : 0.003637
  EX_ca2_e : 0.002182
  EX_cl_e : 0.002182
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.700722
  EX_co2_e : 35.876486
  EX_h_e : 6.759472
  EX_etoh_e : 0.557094
  Auxiliary production reaction : 0.379189
  EX_ac_e : 0.244095
  EX_hxan_e : 0.000469
  DM_5drib_c : 0.000281
  DM_4crsol_c : 0.000093

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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