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 : ugmd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b2836 b2242 b4382 b3831 b4384 b3614 b0910 b2781 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0651 b2162 b1759 b2210 b1415 b4138 b4123 b0621 b2406 b2492 b0904 b2197 b3028 b3918 b4042 b1206 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497267 (mmol/gDw/h)
  Minimum Production Rate : 0.262629 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.367418
  EX_o2_e : 277.819619
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.388857
  EX_pi_e : 1.004925
  EX_so4_e : 0.125222
  EX_k_e : 0.097063
  EX_mg2_e : 0.004314
  EX_cl_e : 0.002588
  EX_ca2_e : 0.002588
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992013
  EX_h2o_e : 547.574492
  EX_co2_e : 27.963252
  EX_succ_e : 0.518546
  Auxiliary production reaction : 0.262629
  EX_ura_e : 0.090007
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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