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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b3399 b4382 b4069 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2926 b0160 b2407 b0517 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b1701 b1805 b3945 b0507 b3709 b2406 b3161 b0112 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0594 b3447   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.579188 (mmol/gDw/h)
  Minimum Production Rate : 0.732801 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.477585
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.462623
  EX_pi_e : 2.024289
  EX_so4_e : 0.145851
  EX_k_e : 0.113053
  EX_fe2_e : 0.009302
  EX_mg2_e : 0.005024
  EX_cl_e : 0.003015
  EX_ca2_e : 0.003015
  EX_cu2_e : 0.000411
  EX_mn2_e : 0.000400
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.887970
  EX_co2_e : 26.977354
  EX_h_e : 8.108832
  EX_ac_e : 1.312379
  Auxiliary production reaction : 0.732801
  EX_alltn_e : 0.002261
  DM_5drib_c : 0.002002
  DM_4crsol_c : 0.001742

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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