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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b3942 b1732 b3846 b2341 b1241 b4069 b2930 b4232 b3697 b3925 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b2690 b2463 b0207 b3012 b2210 b3551 b2799 b1602 b4219 b1832 b1778 b4381 b3915 b4064 b4464 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1710 b2480 b1771 b1517 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.322844 (mmol/gDw/h)
  Minimum Production Rate : 1.063431 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.048702
  EX_o2_e : 280.054451
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.613549
  EX_pi_e : 2.438279
  EX_so4_e : 0.081299
  EX_k_e : 0.063017
  EX_mg2_e : 0.002801
  EX_ca2_e : 0.001680
  EX_cl_e : 0.001680
  EX_cu2_e : 0.000229
  EX_mn2_e : 0.000223
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994815
  EX_h2o_e : 547.048200
  EX_co2_e : 29.344613
  EX_ac_e : 3.242945
  Auxiliary production reaction : 1.063431
  EX_fum_e : 0.336659
  DM_mththf_c : 0.000145
  DM_5drib_c : 0.000073
  DM_4crsol_c : 0.000072

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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