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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3708 b3008 b0871 b0030 b2407 b2797 b3117 b1814 b4471 b2943 b2868 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.777963 (mmol/gDw/h)
  Minimum Production Rate : 0.158677 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.967548
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.120161
  EX_pi_e : 0.750428
  EX_so4_e : 0.195907
  EX_k_e : 0.151853
  EX_fe2_e : 0.012495
  EX_mg2_e : 0.006749
  EX_ca2_e : 0.004049
  EX_cl_e : 0.004049
  EX_cu2_e : 0.000552
  EX_mn2_e : 0.000538
  EX_zn2_e : 0.000265
  EX_ni2_e : 0.000251
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 49.328529
  EX_co2_e : 27.168667
  EX_h_e : 7.866461
  Auxiliary production reaction : 0.159201
  EX_xan_e : 0.020356
  DM_mththf_c : 0.000349
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000173

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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