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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b2799 b3945 b1602 b4381 b2406 b3915 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b3662 b1517 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.464390 (mmol/gDw/h)
  Minimum Production Rate : 0.363230 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.616403
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.105063
  EX_pi_e : 0.811183
  EX_so4_e : 0.116943
  EX_k_e : 0.090646
  EX_fe3_e : 0.007459
  EX_mg2_e : 0.004029
  EX_ca2_e : 0.002417
  EX_cl_e : 0.002417
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.684963
  EX_co2_e : 37.327810
  EX_h_e : 5.271281
  Auxiliary production reaction : 0.363230
  EX_ac_e : 0.270361
  EX_etoh_e : 0.081754
  DM_mththf_c : 0.000208
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000104

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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