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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b3708 b2297 b2458 b2926 b3617 b1004 b3713 b1109 b0046 b3124 b3236 b2797 b3117 b1814 b4471 b1033 b0261 b1602 b2913 b4381 b2789 b3127 b0114 b0755 b3612 b1539 b2492 b0904 b1380 b1695 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.426525 (mmol/gDw/h)
  Minimum Production Rate : 0.159713 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.782867
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.925934
  EX_pi_e : 0.411429
  EX_so4_e : 0.107408
  EX_k_e : 0.083255
  EX_fe2_e : 0.006850
  EX_mg2_e : 0.003700
  EX_ca2_e : 0.002220
  EX_cl_e : 0.002220
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000295
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.036323
  EX_co2_e : 38.133975
  EX_h_e : 6.338289
  EX_ac_e : 1.620495
  DM_oxam_c : 0.319499
  Auxiliary production reaction : 0.159713
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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