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 : dtdp4d6dm_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b0474 b2518 b3831 b2744 b3752 b2930 b4232 b3697 b3925 b4152 b2926 b2781 b3844 b1612 b1611 b4122 b2690 b1759 b4374 b4161 b2361 b2291 b0411 b3945 b4138 b4123 b0621 b0452 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.611381 (mmol/gDw/h)
  Minimum Production Rate : 0.090627 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.527011
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.469988
  EX_fe3_e : 2.321723
  EX_pi_e : 0.770997
  EX_so4_e : 0.153958
  EX_k_e : 0.119337
  EX_mg2_e : 0.005304
  EX_ca2_e : 0.003182
  EX_cl_e : 0.003182
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.776170
  EX_co2_e : 29.533658
  EX_h_e : 9.900292
  EX_fe2_e : 2.311903
  EX_succ_e : 0.637544
  EX_ura_e : 0.342933
  Auxiliary production reaction : 0.090627
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000136

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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