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

Gene deletion strategy (107 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b4269 b0493 b3846 b3588 b3003 b3011 b1241 b4384 b3403 b0871 b2925 b2097 b1850 b3844 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b1779 b2690 b3908 b1656 b1982 b1302 b2662 b4139 b1623 b2799 b3945 b1602 b2913 b2789 b3127 b2975 b3603 b2492 b0904 b1380 b0514 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430383 (mmol/gDw/h)
  Minimum Production Rate : 0.044353 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.789055
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.648096
  EX_pi_e : 0.415150
  EX_so4_e : 0.108379
  EX_k_e : 0.084008
  EX_mg2_e : 0.003734
  EX_fe2_e : 0.003552
  EX_fe3_e : 0.003360
  EX_ca2_e : 0.002240
  EX_cl_e : 0.002240
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.406032
  EX_co2_e : 36.998144
  EX_h_e : 4.002240
  EX_acald_e : 2.535255
  Auxiliary production reaction : 0.044353
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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