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 : prbamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b4384 b2744 b2930 b4232 b3697 b3925 b0871 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b2690 b1982 b1033 b2440 b1623 b0261 b0411 b2799 b3945 b1602 b0153 b4381 b0590 b2406 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379252 (mmol/gDw/h)
  Minimum Production Rate : 0.004600 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.200309
  EX_o2_e : 280.427071
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.160281
  EX_pi_e : 0.375029
  EX_so4_e : 0.095503
  EX_k_e : 0.074027
  EX_mg2_e : 0.003290
  EX_ca2_e : 0.001974
  EX_cl_e : 0.001974
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993909
  EX_h2o_e : 543.992366
  EX_co2_e : 28.578394
  EX_pyr_e : 5.244490
  EX_hxan_e : 0.010348
  Auxiliary production reaction : 0.004600
  DM_5drib_c : 0.000254
  DM_4crsol_c : 0.000085

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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