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 (54 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b0474 b2518 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b3915 b2197 b3918 b4042 b1695 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.579982 (mmol/gDw/h)
  Minimum Production Rate : 0.611676 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.016761
  EX_o2_e : 268.039009
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.086344
  EX_pi_e : 0.559454
  EX_so4_e : 0.146051
  EX_k_e : 0.113208
  EX_mg2_e : 0.005031
  EX_ca2_e : 0.003019
  EX_cl_e : 0.003019
  EX_cu2_e : 0.000411
  EX_mn2_e : 0.000401
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990685
  EX_h2o_e : 540.921499
  EX_co2_e : 22.337491
  Auxiliary production reaction : 0.611676
  EX_succ_e : 0.604801
  EX_ura_e : 0.411293
  EX_hxa_e : 0.000954
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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