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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b2066 b1241 b4069 b4384 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b0477 b4139 b2498 b4015 b2799 b3945 b1602 b0153 b2913 b2406 b2975 b3603 b0529 b2492 b0904 b2954 b3035 b1380 b3662 b1518 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462650 (mmol/gDw/h)
  Minimum Production Rate : 0.243282 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.902513
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.996583
  EX_pi_e : 0.446275
  EX_so4_e : 0.116505
  EX_k_e : 0.090306
  EX_mg2_e : 0.004013
  EX_fe2_e : 0.003818
  EX_fe3_e : 0.003612
  EX_ca2_e : 0.002408
  EX_cl_e : 0.002408
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.984688
  EX_co2_e : 38.769183
  EX_h_e : 4.767258
  EX_ac_e : 0.269348
  Auxiliary production reaction : 0.243282
  DM_mththf_c : 0.242972
  DM_5drib_c : 0.000310
  DM_4crsol_c : 0.000103

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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