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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2937 b0937 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b2799 b3945 b1602 b4388 b2406 b2789 b3127 b0529 b2492 b0904 b2954 b1298 b3029 b1380 b2660 b3662 b1985 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396228 (mmol/gDw/h)
  Minimum Production Rate : 0.600788 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.682749
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.684594
  EX_pi_e : 0.382203
  EX_so4_e : 0.099778
  EX_k_e : 0.077341
  EX_mg2_e : 0.003437
  EX_fe2_e : 0.003270
  EX_fe3_e : 0.003094
  EX_ca2_e : 0.002062
  EX_cl_e : 0.002062
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 52.998163
  EX_co2_e : 38.326484
  EX_h_e : 6.049161
  Auxiliary production reaction : 0.600788
  EX_ade_e : 0.000443
  DM_5drib_c : 0.000266
  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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