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 : udpg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3916 b4382 b0474 b2518 b3831 b4384 b3752 b4152 b2779 b2781 b1851 b1612 b1611 b4122 b1759 b4161 b4138 b4123 b0621 b2406 b1723 b3825 b3918 b4042 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.653744 (mmol/gDw/h)
  Minimum Production Rate : 0.345272 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.382539
  EX_o2_e : 274.426064
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.987585
  EX_pi_e : 1.321149
  EX_so4_e : 0.164626
  EX_k_e : 0.127606
  EX_mg2_e : 0.005671
  EX_cl_e : 0.003403
  EX_ca2_e : 0.003403
  EX_cu2_e : 0.000464
  EX_mn2_e : 0.000452
  EX_zn2_e : 0.000223
  EX_ni2_e : 0.000211
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989500
  EX_h2o_e : 546.426672
  EX_co2_e : 24.787531
  EX_succ_e : 0.681719
  Auxiliary production reaction : 0.345272
  EX_ura_e : 0.118330
  DM_5drib_c : 0.000147
  DM_4crsol_c : 0.000146

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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