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 : nicrnt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b0474 b2518 b3831 b2930 b4232 b3697 b3925 b4152 b2297 b2458 b2781 b0030 b1612 b1611 b4122 b0907 b0651 b2162 b1779 b2690 b1759 b3962 b4267 b1033 b4161 b1415 b4014 b2976 b0614 b0726 b3945 b4138 b4123 b0621 b2406 b0452 b1539 b1380 b3918 b0325 b4266 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.394325 (mmol/gDw/h)
  Minimum Production Rate : 0.208261 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.874394
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.609686
  EX_pi_e : 0.588629
  EX_so4_e : 0.099299
  EX_k_e : 0.076969
  EX_fe2_e : 0.006333
  EX_mg2_e : 0.003421
  EX_ca2_e : 0.002052
  EX_cl_e : 0.002052
  EX_cu2_e : 0.000280
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 45.559268
  EX_co2_e : 31.677688
  EX_h_e : 8.754318
  EX_succ_e : 1.653849
  EX_ac_e : 1.472220
  Auxiliary production reaction : 0.208261
  EX_ura_e : 0.071374
  EX_dxylnt_e : 0.000176
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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