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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4382 b0586 b2502 b4384 b2744 b3708 b3008 b0871 b2797 b3117 b1814 b4471 b3665 b0675 b2361 b0261 b3709 b4381 b2406 b3161 b0112 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.738704 (mmol/gDw/h)
  Minimum Production Rate : 0.511156 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.178315
  EX_o2_e : 272.988651
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.489098
  EX_pi_e : 1.223714
  EX_so4_e : 0.186020
  EX_k_e : 0.144190
  EX_mg2_e : 0.006408
  EX_ca2_e : 0.003845
  EX_cl_e : 0.003845
  EX_cu2_e : 0.000524
  EX_mn2_e : 0.000510
  EX_zn2_e : 0.000252
  EX_ni2_e : 0.000239
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988136
  EX_h2o_e : 546.113854
  EX_co2_e : 25.079183
  Auxiliary production reaction : 0.511156
  DM_5drib_c : 0.000166
  DM_4crsol_c : 0.000165

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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