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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2297 b2458 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b1759 b3946 b0825 b4161 b4014 b2976 b0411 b4138 b4123 b0621 b2913 b1380 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.587754 (mmol/gDw/h)
  Minimum Production Rate : 0.310419 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.226385
  EX_o2_e : 277.271001
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.181306
  EX_pi_e : 0.566951
  EX_so4_e : 0.148008
  EX_k_e : 0.114726
  EX_mg2_e : 0.005099
  EX_cl_e : 0.003059
  EX_ca2_e : 0.003059
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000406
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990560
  EX_h2o_e : 546.119575
  EX_co2_e : 27.595981
  EX_ac_e : 1.304234
  EX_succ_e : 0.612905
  Auxiliary production reaction : 0.310419
  EX_ura_e : 0.106385
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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