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 (64 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3708 b3926 b0871 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b1033 b0505 b1602 b2913 b4381 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1380 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.503189 (mmol/gDw/h)
  Minimum Production Rate : 0.097367 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.914400
  EX_o2_e : 287.989639
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.883148
  EX_pi_e : 0.485379
  EX_so4_e : 0.126713
  EX_k_e : 0.098219
  EX_mg2_e : 0.004365
  EX_cl_e : 0.002619
  EX_ca2_e : 0.002619
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991918
  EX_h2o_e : 553.072556
  EX_co2_e : 38.780396
  Auxiliary production reaction : 0.110872
  DM_oxam_c : 0.005266
  DM_mththf_c : 0.000225
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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