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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b1479 b0871 b2925 b2097 b2926 b0030 b2407 b3236 b2883 b2463 b3962 b3616 b3589 b3946 b2210 b0825 b4267 b0675 b1415 b3551 b1014 b0822 b2799 b4219 b1832 b1778 b4381 b2406 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b0508 b4266 b3662 b1813 b1517 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.294735 (mmol/gDw/h)
  Minimum Production Rate : 0.389985 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.093054
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.580369
  EX_pi_e : 0.674288
  EX_so4_e : 0.074220
  EX_k_e : 0.057530
  EX_mg2_e : 0.002557
  EX_fe2_e : 0.002432
  EX_fe3_e : 0.002301
  EX_cl_e : 0.001534
  EX_ca2_e : 0.001534
  EX_cu2_e : 0.000209
  EX_mn2_e : 0.000204
  EX_zn2_e : 0.000101
  EX_ni2_e : 0.000095

Product: (mmol/gDw/h)
  EX_h2o_e : 45.530302
  EX_co2_e : 27.222514
  EX_h_e : 10.059219
  EX_pyr_e : 4.951321
  EX_acald_e : 0.738592
  Auxiliary production reaction : 0.389985
  EX_ade_e : 0.089467
  EX_dxylnt_e : 0.000197
  DM_mththf_c : 0.000132
  DM_5drib_c : 0.000066
  DM_4crsol_c : 0.000066

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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