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 (73 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b0871 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b3915 b0529 b2492 b0904 b1380 b4042 b2660 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.334089 (mmol/gDw/h)
  Minimum Production Rate : 0.012053 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.442135
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.523985
  EX_pi_e : 0.322264
  EX_so4_e : 0.084130
  EX_k_e : 0.065212
  EX_fe3_e : 0.017419
  EX_mg2_e : 0.002898
  EX_ca2_e : 0.001739
  EX_cl_e : 0.001739
  EX_cu2_e : 0.000237
  EX_mn2_e : 0.000231
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 50.881508
  EX_co2_e : 34.384098
  EX_h_e : 6.051228
  EX_acald_e : 0.867494
  EX_ade_e : 0.573528
  DM_5drib_c : 0.573379
  DM_4crsol_c : 0.549122
  Auxiliary production reaction : 0.012053

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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