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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2502 b2744 b1278 b3708 b1479 b2297 b2458 b2926 b3617 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b4267 b4374 b0675 b2361 b2291 b3551 b1014 b4014 b0261 b2976 b0822 b0507 b3709 b1907 b4219 b1832 b1778 b3161 b0112 b0452 b4265 b2975 b0114 b3603 b0306 b1539 b3605 b2492 b0904 b1533 b1380 b0325 b1710 b2480 b0508 b1473 b0594 b4266 b1813 b0221 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277123 (mmol/gDw/h)
  Minimum Production Rate : 0.294301 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.509996
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.293981
  EX_pi_e : 1.150219
  EX_so4_e : 0.604742
  EX_k_e : 0.054093
  EX_mg2_e : 0.002404
  EX_fe2_e : 0.002287
  EX_fe3_e : 0.002164
  EX_ca2_e : 0.001442
  EX_cl_e : 0.001442
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000191
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 49.742408
  EX_co2_e : 33.997367
  EX_h_e : 5.193995
  EX_ac_e : 2.002458
  Auxiliary production reaction : 0.294301
  EX_met__L_e : 0.240655
  DM_oxam_c : 0.000310
  DM_5drib_c : 0.000186
  EX_dxylnt_e : 0.000185
  DM_4crsol_c : 0.000062

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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