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 : udpLa4n_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2744 b3614 b0910 b4152 b2781 b1612 b1611 b4122 b1759 b3449 b4374 b0675 b2361 b2291 b4388 b4138 b4123 b0621 b3453 b0755 b3612 b3918 b1912 b2240 b1813 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.455631 (mmol/gDw/h)
  Minimum Production Rate : 0.240639 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.690969
  EX_o2_e : 285.447187
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.807631
  EX_pi_e : 0.920782
  EX_so4_e : 0.114737
  EX_k_e : 0.088936
  EX_mg2_e : 0.003953
  EX_ca2_e : 0.002372
  EX_cl_e : 0.002372
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000315
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992682
  EX_h2o_e : 551.021272
  EX_co2_e : 35.699114
  EX_succ_e : 0.475128
  Auxiliary production reaction : 0.240639
  EX_ura_e : 0.082471
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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