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 : ttdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b0474 b2518 b2744 b4152 b2781 b0767 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4388 b4138 b4123 b0621 b4381 b2406 b2197 b3918 b1912 b1695 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406674 (mmol/gDw/h)
  Minimum Production Rate : 0.428897 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 986.681129
  EX_o2_e : 266.207572
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.968829
  EX_pi_e : 0.392280
  EX_so4_e : 0.102409
  EX_k_e : 0.079380
  EX_mg2_e : 0.003528
  EX_ca2_e : 0.002117
  EX_cl_e : 0.002117
  EX_cu2_e : 0.000288
  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_fe3_e : 999.993468
  EX_h2o_e : 531.609055
  EX_co2_e : 19.007148
  EX_ac_e : 7.721154
  Auxiliary production reaction : 0.428897
  EX_succ_e : 0.424076
  EX_ura_e : 0.288392
  EX_hxa_e : 0.000669
  DM_5drib_c : 0.000092
  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.

Last updated: 21-Sep-2023
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