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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b3399 b4382 b4069 b4384 b2744 b2297 b2458 b2925 b2097 b2926 b0160 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b4139 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b3029 b1380 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.389962 (mmol/gDw/h)
  Minimum Production Rate : 0.042590 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.059859
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.424507
  EX_pi_e : 0.461339
  EX_so4_e : 0.098200
  EX_k_e : 0.076118
  EX_fe3_e : 0.006263
  EX_mg2_e : 0.003383
  EX_ca2_e : 0.002030
  EX_cl_e : 0.002030
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 43.677954
  EX_co2_e : 32.787007
  EX_h_e : 8.958131
  EX_ac_e : 5.240534
  Auxiliary production reaction : 0.042590
  EX_glyclt_e : 0.000436
  DM_5drib_c : 0.000262
  DM_4crsol_c : 0.000087

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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