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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b4152 b2297 b2458 b3617 b1612 b1611 b2883 b4122 b1623 b3665 b0411 b4138 b4123 b0621 b4381 b2406 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3662 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.440321 (mmol/gDw/h)
  Minimum Production Rate : 0.208233 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.390419
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.050719
  EX_pi_e : 0.841203
  EX_so4_e : 0.110882
  EX_k_e : 0.085948
  EX_fe2_e : 0.007072
  EX_mg2_e : 0.003820
  EX_cl_e : 0.002292
  EX_ca2_e : 0.002292
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 39.598166
  EX_co2_e : 21.230691
  EX_h_e : 6.417033
  EX_succ_e : 0.482206
  EX_thym_e : 0.335296
  EX_ac_e : 0.319719
  Auxiliary production reaction : 0.208233
  DM_mththf_c : 0.000197
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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.

Last updated: 21-Sep-2023
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