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 : damp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b2744 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b3617 b0160 b2690 b1982 b0675 b2361 b3945 b4381 b0114 b0529 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.615074 (mmol/gDw/h)
  Minimum Production Rate : 0.111674 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.062846
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.217620
  EX_pi_e : 0.704978
  EX_so4_e : 0.154888
  EX_k_e : 0.120058
  EX_fe2_e : 0.009879
  EX_mg2_e : 0.005336
  EX_ca2_e : 0.003201
  EX_cl_e : 0.003201
  EX_cu2_e : 0.000436
  EX_mn2_e : 0.000425
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.837933
  EX_co2_e : 27.032193
  EX_h_e : 8.433171
  EX_pyr_e : 2.190243
  Auxiliary production reaction : 0.111674
  DM_oxam_c : 0.016508
  DM_mththf_c : 0.000276
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000137

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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