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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b0474 b2518 b2744 b4152 b2779 b2781 b1850 b1612 b1611 b4122 b1779 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2197 b2835 b1380 b3918 b4042 b0494 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.604825 (mmol/gDw/h)
  Minimum Production Rate : 0.075392 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.066631
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.389881
  EX_pi_e : 0.734203
  EX_so4_e : 0.152307
  EX_k_e : 0.118058
  EX_fe2_e : 0.009714
  EX_mg2_e : 0.005247
  EX_ca2_e : 0.003148
  EX_cl_e : 0.003148
  EX_cu2_e : 0.000429
  EX_mn2_e : 0.000418
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.935295
  EX_co2_e : 28.642664
  EX_h_e : 7.525824
  EX_succ_e : 0.630707
  EX_thymd_e : 0.244043
  EX_ura_e : 0.109475
  Auxiliary production reaction : 0.075392
  DM_5drib_c : 0.000136
  DM_4crsol_c : 0.000135

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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