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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b3617 b0160 b1982 b0675 b2361 b0261 b0507 b4381 b2406 b0112 b2975 b0114 b3603 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492014 (mmol/gDw/h)
  Minimum Production Rate : 0.786836 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.107792
  EX_nh4_e : 10.834980
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.048270
  EX_so4_e : 0.123899
  EX_k_e : 0.096038
  EX_fe2_e : 0.007902
  EX_mg2_e : 0.004268
  EX_ca2_e : 0.002561
  EX_cl_e : 0.002561
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.543518
  EX_co2_e : 20.787236
  EX_h_e : 8.481845
  EX_acald_e : 1.233184
  Auxiliary production reaction : 0.786836
  DM_oxam_c : 0.013425
  DM_5drib_c : 0.000330
  DM_4crsol_c : 0.000110

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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