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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b3942 b1732 b4069 b3708 b3926 b2297 b2458 b1004 b3713 b1109 b0046 b2797 b3117 b1814 b4471 b2210 b1602 b4381 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b2835 b1380 b0494 b0516 b1511 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.525828 (mmol/gDw/h)
  Minimum Production Rate : 0.223406 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.122081
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.572519
  EX_pi_e : 0.507217
  EX_so4_e : 0.132414
  EX_k_e : 0.102638
  EX_mg2_e : 0.004562
  EX_fe2_e : 0.004340
  EX_fe3_e : 0.004106
  EX_ca2_e : 0.002737
  EX_cl_e : 0.002737
  EX_cu2_e : 0.000373
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.580979
  EX_co2_e : 36.686719
  EX_h_e : 6.035375
  EX_ac_e : 0.306130
  Auxiliary production reaction : 0.223406
  EX_mththf_e : 0.000236
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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