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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b3553 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b1238 b3124 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b0261 b4381 b2406 b0112 b2789 b3127 b0114 b1539 b2492 b0904 b1533 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.502175 (mmol/gDw/h)
  Minimum Production Rate : 0.500886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.223164
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.930210
  EX_pi_e : 1.987059
  EX_so4_e : 0.627344
  EX_k_e : 0.098021
  EX_fe2_e : 0.008065
  EX_mg2_e : 0.004356
  EX_ca2_e : 0.002614
  EX_cl_e : 0.002614
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.325141
  EX_co2_e : 21.544360
  EX_h_e : 9.278488
  EX_ac_e : 2.659300
  Auxiliary production reaction : 0.500886
  DM_oxam_c : 0.000562
  DM_5drib_c : 0.000337
  EX_glyclt_e : 0.000336
  DM_4crsol_c : 0.000112

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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