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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0871 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b3946 b0825 b1033 b2799 b3945 b1602 b4381 b3915 b2492 b0904 b1380 b2660 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373138 (mmol/gDw/h)
  Minimum Production Rate : 0.369449 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.082896
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.029854
  EX_pi_e : 0.729380
  EX_so4_e : 0.093963
  EX_k_e : 0.072834
  EX_fe3_e : 0.005993
  EX_mg2_e : 0.003237
  EX_ca2_e : 0.001942
  EX_cl_e : 0.001942
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 42.396401
  EX_co2_e : 32.545866
  EX_acald_e : 4.960928
  EX_h_e : 3.434530
  Auxiliary production reaction : 0.369449
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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