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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b4382 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b3617 b0030 b2883 b1982 b0477 b1623 b0261 b2406 b0112 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.502186 (mmol/gDw/h)
  Minimum Production Rate : 0.962426 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.965128
  EX_nh4_e : 10.237948
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.409265
  EX_so4_e : 0.126461
  EX_k_e : 0.098023
  EX_fe2_e : 0.008066
  EX_mg2_e : 0.004356
  EX_ca2_e : 0.002614
  EX_cl_e : 0.002614
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.368414
  EX_co2_e : 19.629163
  EX_h_e : 9.200707
  EX_ac_e : 1.696893
  Auxiliary production reaction : 0.962426
  EX_alltn_e : 0.000562
  DM_5drib_c : 0.000337
  DM_4crsol_c : 0.000112

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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