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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b0411 b2799 b3945 b1602 b3709 b4381 b3161 b0112 b3915 b3654 b3714 b3664 b4064 b4464 b2366 b2492 b0904 b1533 b3821 b1380 b4042 b1473 b2660 b4141 b1798 b1517 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.395782 (mmol/gDw/h)
  Minimum Production Rate : 0.068037 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.333237
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.849297
  EX_pi_e : 0.585873
  EX_so4_e : 0.167700
  EX_k_e : 0.077254
  EX_fe3_e : 0.006358
  EX_mg2_e : 0.003433
  EX_cl_e : 0.002060
  EX_ca2_e : 0.002060
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000273
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 52.680671
  EX_co2_e : 35.673478
  EX_h_e : 7.585827
  EX_ac_e : 1.640114
  EX_xan_e : 0.524663
  Auxiliary production reaction : 0.068033
  DM_mththf_c : 0.000177
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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