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 : fmnh2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (8 of 15: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b3426 b2242 b4384 b3114 b3952 b0903 b2407 b1638 b1779 b3962 b4139 b4267 b1415 b4015 b1014 b3945 b4265 b0529 b1539 b3028 b4321 b0325 b3415 b4476 b0508 b4266 b1813 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406895 (mmol/gDw/h)
  Minimum Production Rate : 0.402142 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.646180
  EX_o2_e : 285.793516
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.003003
  EX_pi_e : 0.794636
  EX_so4_e : 0.102464
  EX_k_e : 0.079423
  EX_mg2_e : 0.003530
  EX_ca2_e : 0.002118
  EX_cl_e : 0.002118
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993465
  EX_h2o_e : 552.431962
  EX_co2_e : 36.462402
  Auxiliary production reaction : 0.402142
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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