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 : ugmda_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3831 b1278 b3614 b0910 b3752 b4152 b2781 b3236 b1612 b1611 b4122 b1638 b3908 b1656 b1759 b2440 b4138 b4123 b0621 b4381 b2406 b3915 b0452 b2492 b0904 b2197 b3918 b0418 b2660 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.485845 (mmol/gDw/h)
  Minimum Production Rate : 0.195087 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.460107
  EX_o2_e : 279.110524
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.363276
  EX_pi_e : 0.858823
  EX_so4_e : 0.122345
  EX_k_e : 0.094834
  EX_mg2_e : 0.004215
  EX_ca2_e : 0.002529
  EX_cl_e : 0.002529
  EX_cu2_e : 0.000344
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992197
  EX_h2o_e : 548.269346
  EX_co2_e : 29.312368
  EX_succ_e : 0.506635
  Auxiliary production reaction : 0.195087
  EX_ura_e : 0.149449
  EX_etha_e : 0.061509
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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