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 : adn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b1478 b4382 b0474 b2518 b1241 b4069 b4384 b2297 b2458 b2926 b2781 b0099 b0160 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b1623 b2799 b3945 b1602 b3915 b4064 b4464 b0529 b2492 b0904 b2954 b1380 b2660 b1511 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.402162 (mmol/gDw/h)
  Minimum Production Rate : 0.631163 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.018463
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.500483
  EX_pi_e : 0.387928
  EX_so4_e : 0.101272
  EX_k_e : 0.078499
  EX_fe3_e : 0.006459
  EX_mg2_e : 0.003489
  EX_ca2_e : 0.002093
  EX_cl_e : 0.002093
  EX_cu2_e : 0.000285
  EX_mn2_e : 0.000278
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.861968
  EX_co2_e : 35.299715
  EX_h_e : 7.798604
  EX_ac_e : 0.939752
  EX_adn_e : 0.631163
  EX_ade_e : 0.000271
  DM_mththf_c : 0.000180
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000090

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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