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 : adprib_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 97: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b0452 b0755 b3612 b0529 b2492 b0904 b1380 b2660 b3662 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359194 (mmol/gDw/h)
  Minimum Production Rate : 0.591060 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.680395
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.836173
  EX_pi_e : 1.528601
  EX_so4_e : 0.090452
  EX_k_e : 0.070112
  EX_fe3_e : 0.005769
  EX_mg2_e : 0.003116
  EX_ca2_e : 0.001870
  EX_cl_e : 0.001870
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 53.730685
  EX_co2_e : 35.969789
  EX_h_e : 5.290092
  Auxiliary production reaction : 0.591060
  EX_ac_e : 0.209118
  EX_hxan_e : 0.000402
  DM_5drib_c : 0.000241
  DM_4crsol_c : 0.000080

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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