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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b4467 b3399 b3942 b1732 b4069 b2744 b3708 b0910 b3926 b0871 b2297 b2458 b2925 b2097 b1238 b1004 b3713 b1109 b0046 b3124 b2883 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b2210 b0595 b0675 b2361 b0261 b0411 b3945 b1602 b4381 b2239 b2406 b2789 b3127 b2975 b0114 b3603 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b0514 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388838 (mmol/gDw/h)
  Minimum Production Rate : 0.494133 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.701559
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.683559
  EX_pi_e : 0.869208
  EX_so4_e : 0.097917
  EX_k_e : 0.075899
  EX_mg2_e : 0.003373
  EX_fe2_e : 0.003209
  EX_fe3_e : 0.003036
  EX_ca2_e : 0.002024
  EX_cl_e : 0.002024
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 44.984099
  EX_co2_e : 27.313451
  EX_h_e : 9.227530
  EX_pyr_e : 4.435311
  Auxiliary production reaction : 0.494133
  EX_ac_e : 0.226376
  EX_hxan_e : 0.000435
  DM_5drib_c : 0.000261
  DM_4crsol_c : 0.000087

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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