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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b1701 b1805 b2799 b3945 b1602 b0153 b2913 b0590 b2406 b2366 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.423877 (mmol/gDw/h)
  Minimum Production Rate : 0.644824 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.561202
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.514680
  EX_pi_e : 1.053698
  EX_so4_e : 0.106741
  EX_k_e : 0.082738
  EX_fe2_e : 0.006808
  EX_mg2_e : 0.003677
  EX_ca2_e : 0.002206
  EX_cl_e : 0.002206
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000293
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.511466
  EX_co2_e : 35.444356
  EX_h_e : 6.184535
  EX_glyclt_e : 0.750987
  Auxiliary production reaction : 0.644824
  EX_ac_e : 0.246775
  EX_ade_e : 0.000474
  DM_5drib_c : 0.000284
  DM_4crsol_c : 0.000095

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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