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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b0160 b1238 b1982 b3616 b3589 b1033 b0675 b2361 b0261 b4381 b0112 b0114 b0509 b3125 b0755 b3612 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.404186 (mmol/gDw/h)
  Minimum Production Rate : 0.774612 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.604248
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.787914
  EX_pi_e : 2.713717
  EX_so4_e : 0.101782
  EX_k_e : 0.078894
  EX_fe2_e : 0.006492
  EX_mg2_e : 0.003506
  EX_ca2_e : 0.002104
  EX_cl_e : 0.002104
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.858042
  EX_co2_e : 23.142229
  EX_h_e : 8.812738
  EX_ac_e : 1.999291
  Auxiliary production reaction : 0.774612
  DM_oxam_c : 0.000452
  DM_5drib_c : 0.000271
  EX_glyclt_e : 0.000270
  DM_4crsol_c : 0.000090

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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