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 : camp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b4382 b1241 b0351 b4069 b4384 b3926 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3616 b3589 b0261 b0411 b1602 b2913 b2406 b0114 b0529 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.381859 (mmol/gDw/h)
  Minimum Production Rate : 0.731823 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.576941
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.783157
  EX_pi_e : 1.100166
  EX_so4_e : 0.096160
  EX_k_e : 0.074536
  EX_fe2_e : 0.006133
  EX_mg2_e : 0.003313
  EX_cl_e : 0.001988
  EX_ca2_e : 0.001988
  EX_cu2_e : 0.000271
  EX_mn2_e : 0.000264
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 51.159897
  EX_co2_e : 33.229157
  EX_h_e : 6.658276
  EX_etoh_e : 1.666792
  Auxiliary production reaction : 0.731823
  EX_ac_e : 0.222313
  DM_5drib_c : 0.000256
  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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