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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1478 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2925 b2097 b3617 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b1982 b0675 b2361 b0261 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b2660 b1771 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.300237 (mmol/gDw/h)
  Minimum Production Rate : 0.295426 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.841835
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.431738
  EX_pi_e : 0.880462
  EX_so4_e : 0.075606
  EX_k_e : 0.058604
  EX_fe2_e : 0.004822
  EX_mg2_e : 0.002605
  EX_ca2_e : 0.001563
  EX_cl_e : 0.001563
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000207
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 46.367420
  EX_co2_e : 30.977773
  EX_h_e : 5.531843
  EX_12ppd__S_e : 1.514533
  EX_thymd_e : 0.559941
  Auxiliary production reaction : 0.295426
  EX_ac_e : 0.174794
  EX_hxan_e : 0.000336
  DM_5drib_c : 0.000201
  DM_4crsol_c : 0.000067

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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