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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0512 b0871 b2779 b2925 b2097 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b3945 b4381 b0452 b0114 b2366 b2492 b0904 b1533 b3927 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406998 (mmol/gDw/h)
  Minimum Production Rate : 0.092282 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.635106
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.771024
  EX_pi_e : 0.484874
  EX_so4_e : 0.102490
  EX_k_e : 0.079443
  EX_fe2_e : 0.006537
  EX_mg2_e : 0.003531
  EX_ca2_e : 0.002118
  EX_cl_e : 0.002118
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 39.624238
  EX_co2_e : 27.850330
  EX_h_e : 8.951015
  EX_glyc__R_e : 4.835874
  Auxiliary production reaction : 0.092282
  EX_alltn_e : 0.001589
  DM_mththf_c : 0.001316
  DM_5drib_c : 0.000273
  DM_4crsol_c : 0.000091

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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