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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4382 b0474 b2518 b1241 b0351 b4069 b2502 b4384 b2744 b4152 b2297 b2458 b2926 b2781 b0099 b1612 b1611 b2883 b4122 b0907 b3616 b3589 b4138 b4123 b0621 b0114 b0529 b2492 b0904 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.451783 (mmol/gDw/h)
  Minimum Production Rate : 1.732872 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.622975
  EX_o2_e : 273.172521
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.519975
  EX_pi_e : 3.901537
  EX_so4_e : 0.113768
  EX_k_e : 0.088185
  EX_mg2_e : 0.003919
  EX_ca2_e : 0.002352
  EX_cl_e : 0.002352
  EX_cu2_e : 0.000320
  EX_mn2_e : 0.000312
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992744
  EX_h2o_e : 544.353528
  EX_co2_e : 26.888064
  Auxiliary production reaction : 1.732872
  EX_ac_e : 1.368490
  EX_succ_e : 0.471115
  EX_ura_e : 0.320381
  DM_mththf_c : 0.000202
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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