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 : pgp160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b2242 b3553 b0474 b2518 b2744 b2781 b3844 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b3915 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b4042 b1695 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452862 (mmol/gDw/h)
  Minimum Production Rate : 0.238207 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.482348
  EX_o2_e : 275.353259
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.532561
  EX_pi_e : 0.913247
  EX_so4_e : 0.114041
  EX_k_e : 0.088396
  EX_mg2_e : 0.003929
  EX_ca2_e : 0.002357
  EX_cl_e : 0.002357
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992725
  EX_h2o_e : 543.926164
  EX_co2_e : 29.179881
  EX_succ_e : 0.472241
  EX_ura_e : 0.320843
  Auxiliary production reaction : 0.238207
  EX_hxa_e : 0.001335
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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