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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b4384 b2744 b0871 b1004 b3713 b1109 b0046 b3236 b1982 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b3915 b1727 b0755 b3612 b0529 b2492 b0904 b2835 b1380 b0494 b1695 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.471128 (mmol/gDw/h)
  Minimum Production Rate : 0.041127 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.762727
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.294911
  EX_pi_e : 0.536653
  EX_so4_e : 0.118640
  EX_k_e : 0.091961
  EX_fe3_e : 0.007569
  EX_mg2_e : 0.004087
  EX_ca2_e : 0.002452
  EX_cl_e : 0.002452
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000326
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.641032
  EX_co2_e : 37.860909
  EX_h_e : 4.502149
  EX_etoh_e : 1.194434
  Auxiliary production reaction : 0.041100
  EX_hxan_e : 0.000317
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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