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 (71 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4382 b4069 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b0030 b2407 b0583 b2883 b2690 b2797 b3117 b1814 b4471 b3449 b0261 b3945 b4381 b2406 b0452 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.721763 (mmol/gDw/h)
  Minimum Production Rate : 0.051464 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.007645
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.714443
  EX_pi_e : 0.747682
  EX_so4_e : 0.615752
  EX_k_e : 0.140883
  EX_fe2_e : 0.011592
  EX_mg2_e : 0.006261
  EX_ca2_e : 0.003757
  EX_cl_e : 0.003757
  EX_cu2_e : 0.000512
  EX_mn2_e : 0.000499
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 46.983524
  EX_co2_e : 26.033365
  EX_h_e : 7.588977
  EX_ac_e : 0.854198
  EX_cgly_e : 0.433998
  Auxiliary production reaction : 0.051464
  DM_5drib_c : 0.000162
  DM_4crsol_c : 0.000161

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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