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 (56 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4384 b0871 b2925 b2097 b2926 b2407 b3236 b2690 b3962 b3616 b3589 b2210 b4267 b2799 b0726 b3945 b0114 b0509 b3125 b2492 b0904 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.423283 (mmol/gDw/h)
  Minimum Production Rate : 0.341301 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.283556
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.571418
  EX_pi_e : 0.408301
  EX_so4_e : 0.106591
  EX_k_e : 0.082622
  EX_fe2_e : 0.006798
  EX_mg2_e : 0.003672
  EX_ca2_e : 0.002203
  EX_cl_e : 0.002203
  EX_cu2_e : 0.000300
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.715925
  EX_co2_e : 28.518104
  EX_h_e : 8.250685
  EX_pyr_e : 4.020093
  Auxiliary production reaction : 0.341301
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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