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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b3399 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1623 b0261 b3945 b1602 b0153 b4381 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b3035 b1380 b2660 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444541 (mmol/gDw/h)
  Minimum Production Rate : 0.193719 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.240010
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.849029
  EX_pi_e : 0.428807
  EX_so4_e : 0.111944
  EX_k_e : 0.086771
  EX_fe2_e : 0.007140
  EX_mg2_e : 0.003856
  EX_ca2_e : 0.002314
  EX_cl_e : 0.002314
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.908761
  EX_co2_e : 37.243719
  EX_h_e : 4.585168
  EX_12ppd__S_e : 1.181736
  EX_ac_e : 0.258806
  Auxiliary production reaction : 0.193719
  EX_hxan_e : 0.011632
  EX_ade_e : 0.000299
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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
Contact