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 : mththf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1478 b1241 b0351 b4384 b0871 b2925 b2097 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b1982 b0411 b2799 b3945 b1602 b0153 b2913 b4381 b0584 b0529 b2492 b0904 b3927 b1380 b1601 b1518 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442486 (mmol/gDw/h)
  Minimum Production Rate : 0.017210 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.412216
  EX_o2_e : 284.093772
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.848833
  EX_pi_e : 0.426824
  EX_so4_e : 0.111427
  EX_k_e : 0.086370
  EX_mg2_e : 0.003839
  EX_ca2_e : 0.002303
  EX_cl_e : 0.002303
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992893
  EX_h2o_e : 544.612424
  EX_co2_e : 32.773597
  EX_glyclt_e : 4.444917
  EX_hxan_e : 0.017507
  DM_mththf_c : 0.017407
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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