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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b4382 b4384 b3708 b3008 b0871 b2779 b2926 b0030 b2407 b0121 b1982 b2797 b3117 b1814 b4471 b3449 b1033 b0261 b3709 b2406 b3161 b0112 b2789 b3127 b0114 b0886 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b1473 b0494 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.668219 (mmol/gDw/h)
  Minimum Production Rate : 0.153380 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.383854
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.291110
  EX_pi_e : 0.644568
  EX_so4_e : 0.168271
  EX_k_e : 0.130432
  EX_fe2_e : 0.010732
  EX_mg2_e : 0.005797
  EX_cl_e : 0.003478
  EX_ca2_e : 0.003478
  EX_cu2_e : 0.000474
  EX_mn2_e : 0.000462
  EX_zn2_e : 0.000228
  EX_ni2_e : 0.000216
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.910252
  EX_co2_e : 29.502114
  EX_h_e : 7.368393
  Auxiliary production reaction : 0.153380
  DM_oxam_c : 0.000748
  DM_5drib_c : 0.000448
  DM_4crsol_c : 0.000149

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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