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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1478 b2066 b1241 b4069 b4384 b2297 b2458 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b2498 b1033 b2799 b3945 b1602 b2913 b2223 b3915 b0529 b2492 b0904 b1380 b1517 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.487629 (mmol/gDw/h)
  Minimum Production Rate : 0.015940 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.324797
  EX_o2_e : 287.705876
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.169303
  EX_pi_e : 0.486310
  EX_so4_e : 0.122795
  EX_k_e : 0.095182
  EX_mg2_e : 0.004230
  EX_ca2_e : 0.002538
  EX_cl_e : 0.002538
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992168
  EX_h2o_e : 553.096522
  EX_co2_e : 38.192275
  EX_ac_e : 0.283891
  EX_hxan_e : 0.225328
  Auxiliary production reaction : 0.015940
  EX_ade_e : 0.000328
  EX_mththf_e : 0.000218
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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