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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 58
  Gene deletion: b3553 b3399 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b2502 b2744 b1479 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b3844 b3236 b2690 b2463 b3962 b1982 b2210 b4267 b1033 b4374 b0675 b2361 b2291 b1415 b3551 b1014 b0822 b4388 b4219 b1832 b1778 b0112 b2868 b1727 b0114 b0529 b1539 b2492 b0904 b1380 b0325 b1710 b2480 b4042 b1511 b4266 b1813 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.257228 (mmol/gDw/h)
  Minimum Production Rate : 0.414606 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.867044
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.244618
  EX_pi_e : 1.077336
  EX_so4_e : 0.064775
  EX_k_e : 0.050209
  EX_fe2_e : 0.004131
  EX_mg2_e : 0.002231
  EX_ca2_e : 0.001339
  EX_cl_e : 0.001339
  EX_cu2_e : 0.000182
  EX_mn2_e : 0.000178
  EX_zn2_e : 0.000088
  EX_ni2_e : 0.000083

Product: (mmol/gDw/h)
  EX_h2o_e : 44.074301
  EX_co2_e : 25.675270
  EX_h_e : 9.873639
  EX_pyr_e : 4.600164
  EX_ac_e : 1.272425
  Auxiliary production reaction : 0.414606
  EX_ade_e : 0.078709
  DM_mththf_c : 0.078537
  DM_5drib_c : 0.000173
  EX_dxylnt_e : 0.000172
  DM_4crsol_c : 0.000057

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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