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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (118 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 67
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2925 b2097 b0160 b0583 b2690 b3962 b1982 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b3665 b4374 b0675 b2361 b2291 b1014 b4014 b0261 b2976 b0822 b2799 b3709 b1907 b3161 b0112 b3915 b0452 b1727 b4265 b2975 b0114 b3603 b0509 b3125 b0755 b3612 b0306 b1539 b3605 b2492 b0904 b2954 b1533 b1380 b4042 b1473 b4266 b1985 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.253303 (mmol/gDw/h)
  Minimum Production Rate : 0.136068 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.279788
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.311146
  EX_so4_e : 0.685458
  EX_pi_e : 0.244338
  EX_k_e : 0.049443
  EX_fe3_e : 0.004069
  EX_mg2_e : 0.002197
  EX_ca2_e : 0.001318
  EX_cl_e : 0.001318
  EX_cu2_e : 0.000180
  EX_mn2_e : 0.000175
  EX_zn2_e : 0.000086
  EX_ni2_e : 0.000082

Product: (mmol/gDw/h)
  EX_h2o_e : 41.416873
  EX_co2_e : 31.034654
  EX_h_e : 8.963851
  EX_ac_e : 6.027893
  EX_met__L_e : 0.621671
  EX_dxylnt_e : 0.136228
  Auxiliary production reaction : 0.136058
  EX_ade_e : 0.000283
  DM_5drib_c : 0.000170
  DM_4crsol_c : 0.000056

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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