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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2926 b2407 b3236 b3616 b3589 b2210 b3665 b0511 b0114 b0529 b2492 b0904 b0516 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406914 (mmol/gDw/h)
  Minimum Production Rate : 0.520075 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.037464
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.476302
  EX_pi_e : 1.432661
  EX_so4_e : 0.102469
  EX_k_e : 0.079427
  EX_fe2_e : 0.006535
  EX_mg2_e : 0.003530
  EX_ca2_e : 0.002118
  EX_cl_e : 0.002118
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.854094
  EX_co2_e : 35.864992
  EX_h_e : 6.415499
  EX_ac_e : 1.115020
  Auxiliary production reaction : 0.520075
  EX_ade_e : 0.000274
  DM_mththf_c : 0.000182
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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