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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b2744 b1278 b4152 b2297 b2458 b2781 b3617 b1851 b1612 b1611 b4122 b1779 b1759 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0114 b2492 b0904 b3825 b1380 b3918 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.574017 (mmol/gDw/h)
  Minimum Production Rate : 0.303164 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.402037
  EX_o2_e : 278.309748
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.316621
  EX_pi_e : 0.856864
  EX_so4_e : 0.144549
  EX_k_e : 0.112044
  EX_mg2_e : 0.004980
  EX_cl_e : 0.002988
  EX_ca2_e : 0.002988
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000397
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990781
  EX_h2o_e : 547.778847
  EX_co2_e : 28.475550
  EX_succ_e : 0.598580
  Auxiliary production reaction : 0.303164
  EX_ura_e : 0.103899
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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