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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b3942 b1732 b0238 b0125 b1241 b0351 b3831 b4069 b2744 b3926 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b2463 b0477 b2498 b2210 b2361 b2291 b3551 b1602 b4219 b1832 b1778 b3915 b0529 b2492 b0904 b1380 b1710 b2480 b1771 b1518 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452910 (mmol/gDw/h)
  Minimum Production Rate : 0.784421 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.567533
  EX_o2_e : 283.842670
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.891387
  EX_pi_e : 0.436879
  EX_so4_e : 0.114052
  EX_k_e : 0.088405
  EX_mg2_e : 0.003929
  EX_ca2_e : 0.002357
  EX_cl_e : 0.002357
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992726
  EX_h2o_e : 546.375253
  EX_co2_e : 36.311646
  EX_etoh_e : 1.108429
  EX_glyc_e : 0.784421
  EX_ac_e : 0.263678
  DM_mththf_c : 0.000203
  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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