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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2836 b3399 b4269 b0493 b3588 b3003 b3011 b2744 b0871 b2779 b2926 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b0675 b2361 b0261 b1602 b2913 b4381 b2789 b3127 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482168 (mmol/gDw/h)
  Minimum Production Rate : 0.058273 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.770162
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.259135
  EX_fe3_e : 1.044853
  EX_pi_e : 0.465102
  EX_so4_e : 0.121419
  EX_k_e : 0.094116
  EX_mg2_e : 0.004183
  EX_ca2_e : 0.002510
  EX_cl_e : 0.002510
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.354738
  EX_co2_e : 39.969706
  EX_h_e : 5.585239
  EX_fe2_e : 1.037109
  Auxiliary production reaction : 0.058273
  EX_hxan_e : 0.012941
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000108

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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