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 : ahdt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b1033 b0596 b0261 b0507 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b2835 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494310 (mmol/gDw/h)
  Minimum Production Rate : 1.479164 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.804192
  EX_nh4_e : 12.734882
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.914307
  EX_so4_e : 0.124477
  EX_k_e : 0.096486
  EX_fe2_e : 0.007939
  EX_mg2_e : 0.004288
  EX_ca2_e : 0.002573
  EX_cl_e : 0.002573
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.443870
  EX_co2_e : 21.160265
  EX_h_e : 11.598461
  EX_ac_e : 2.617612
  Auxiliary production reaction : 1.479164
  DM_oxam_c : 0.000553
  DM_5drib_c : 0.000332
  EX_glyclt_e : 0.000331
  DM_4crsol_c : 0.000110

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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