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 : dtdp4addg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 107: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3916 b4382 b0474 b2518 b1241 b0351 b3831 b4384 b4152 b2779 b2781 b3617 b0030 b2407 b1851 b1612 b1611 b4122 b0651 b2162 b1759 b3946 b0825 b4161 b4138 b4123 b0621 b2406 b1723 b3821 b3918 b4042 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.629659 (mmol/gDw/h)
  Minimum Production Rate : 0.332551 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.663184
  EX_o2_e : 274.903901
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.025855
  EX_pi_e : 1.272475
  EX_so4_e : 0.158561
  EX_k_e : 0.122905
  EX_mg2_e : 0.005462
  EX_cl_e : 0.003277
  EX_ca2_e : 0.003277
  EX_cu2_e : 0.000446
  EX_mn2_e : 0.000435
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000203
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989887
  EX_h2o_e : 546.925334
  EX_co2_e : 25.750878
  EX_succ_e : 0.656603
  Auxiliary production reaction : 0.332551
  EX_ura_e : 0.113970
  DM_mththf_c : 0.000282
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000140

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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