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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2925 b2097 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b2799 b3945 b1602 b0507 b0153 b4381 b2406 b1727 b2366 b0529 b2492 b0904 b0591 b1533 b3927 b3821 b1380 b2660 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357915 (mmol/gDw/h)
  Minimum Production Rate : 0.057287 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.911719
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.669469
  EX_pi_e : 0.345247
  EX_so4_e : 0.090130
  EX_k_e : 0.069862
  EX_fe2_e : 0.063035
  EX_mg2_e : 0.003105
  EX_ca2_e : 0.001863
  EX_cl_e : 0.001863
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 44.023131
  EX_co2_e : 33.021281
  EX_h_e : 7.456405
  EX_ac_e : 3.134574
  EX_etoh_e : 1.031607
  EX_ade_e : 0.114974
  DM_5drib_c : 0.114814
  Auxiliary production reaction : 0.057287
  DM_4crsol_c : 0.000080

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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