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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b1241 b0351 b2744 b3708 b3614 b0910 b2930 b4232 b3697 b3925 b4152 b2926 b2781 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b0907 b2690 b1759 b1033 b4374 b0675 b4015 b3945 b1602 b4138 b4123 b0621 b4381 b0452 b0529 b2197 b3029 b1380 b3918 b1912 b2660 b1206 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441481 (mmol/gDw/h)
  Minimum Production Rate : 0.019866 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.890804
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.415793
  EX_pi_e : 0.447543
  EX_so4_e : 0.111174
  EX_k_e : 0.086174
  EX_mg2_e : 0.003830
  EX_fe2_e : 0.003644
  EX_fe3_e : 0.003447
  EX_cl_e : 0.002298
  EX_ca2_e : 0.002298
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.336858
  EX_co2_e : 30.334629
  EX_h_e : 9.078538
  EX_ac_e : 3.450006
  EX_succ_e : 0.460373
  EX_thymd_e : 0.211478
  EX_ura_e : 0.079909
  Auxiliary production reaction : 0.021688
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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