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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b0871 b2297 b2458 b2925 b2097 b2926 b3617 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b2406 b0452 b0114 b2366 b2492 b0904 b1533 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.293148 (mmol/gDw/h)
  Minimum Production Rate : 0.036363 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.505446
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.724877
  EX_pi_e : 0.355499
  EX_so4_e : 0.110184
  EX_k_e : 0.057220
  EX_fe3_e : 0.004708
  EX_mg2_e : 0.002543
  EX_ca2_e : 0.001526
  EX_cl_e : 0.001526
  EX_cu2_e : 0.000208
  EX_mn2_e : 0.000203
  EX_zn2_e : 0.000100
  EX_ni2_e : 0.000095

Product: (mmol/gDw/h)
  EX_h2o_e : 44.727695
  EX_co2_e : 27.075469
  EX_h_e : 10.546248
  EX_pyr_e : 4.650092
  EX_ac_e : 0.784437
  EX_his__L_e : 0.768120
  Auxiliary production reaction : 0.036363
  DM_5drib_c : 0.000197
  DM_4crsol_c : 0.000065

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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