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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b0160 b3616 b3589 b3665 b0675 b2361 b2291 b0261 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.506546 (mmol/gDw/h)
  Minimum Production Rate : 0.748494 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.327662
  EX_nh4_e : 11.601534
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.488618
  EX_so4_e : 0.127558
  EX_k_e : 0.098874
  EX_fe2_e : 0.008136
  EX_mg2_e : 0.004394
  EX_ca2_e : 0.002637
  EX_cl_e : 0.002637
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.966956
  EX_co2_e : 19.940305
  EX_h_e : 11.080131
  EX_thymd_e : 1.194205
  Auxiliary production reaction : 0.748494
  EX_ac_e : 0.294904
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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