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 : hdcea_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b3752 b4152 b2297 b2458 b1702 b2781 b3236 b1612 b1611 b4122 b1759 b2210 b4161 b4138 b4123 b0621 b2406 b2943 b0452 b2150 b2197 b3918 b3437 b4268 b4042 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.567937 (mmol/gDw/h)
  Minimum Production Rate : 0.299393 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.854326
  EX_o2_e : 266.400963
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.939180
  EX_pi_e : 0.547836
  EX_so4_e : 0.143018
  EX_k_e : 0.110857
  EX_mg2_e : 0.004927
  EX_cl_e : 0.002956
  EX_ca2_e : 0.002956
  EX_cu2_e : 0.000403
  EX_mn2_e : 0.000392
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990878
  EX_h2o_e : 536.559530
  EX_co2_e : 18.661040
  EX_ac_e : 4.628739
  EX_succ_e : 0.592241
  EX_ura_e : 0.402752
  Auxiliary production reaction : 0.299393
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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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