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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b1478 b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b1033 b0411 b2799 b3945 b1602 b0507 b2406 b3915 b0452 b3654 b3714 b3664 b4064 b4464 b1539 b2492 b0904 b1533 b1380 b2660 b4141 b1798 b1518 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408874 (mmol/gDw/h)
  Minimum Production Rate : 0.046860 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.303813
  EX_o2_e : 286.838910
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.911866
  EX_pi_e : 0.534969
  EX_so4_e : 0.149819
  EX_k_e : 0.079809
  EX_mg2_e : 0.003547
  EX_cl_e : 0.002128
  EX_ca2_e : 0.002128
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993431
  EX_h2o_e : 552.789977
  EX_co2_e : 36.133899
  EX_ac_e : 1.624082
  EX_xan_e : 0.542018
  Auxiliary production reaction : 0.046856
  DM_mththf_c : 0.000183
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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