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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1478 b0474 b2518 b1241 b4069 b2297 b2458 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b0937 b1033 b2799 b3945 b1602 b2492 b0904 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397061 (mmol/gDw/h)
  Minimum Production Rate : 0.627489 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.910683
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.288230
  EX_pi_e : 0.383008
  EX_so4_e : 0.099988
  EX_k_e : 0.077504
  EX_fe2_e : 0.006377
  EX_mg2_e : 0.003445
  EX_ca2_e : 0.002067
  EX_cl_e : 0.002067
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 42.870805
  EX_co2_e : 32.385510
  EX_h_e : 8.051852
  EX_ac_e : 3.776004
  Auxiliary production reaction : 0.627489
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000089

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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