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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b2779 b2926 b3617 b0160 b1982 b1033 b0675 b2361 b2291 b0261 b2913 b4381 b0112 b2789 b3127 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425406 (mmol/gDw/h)
  Minimum Production Rate : 0.691447 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.505822
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.434959
  EX_pi_e : 1.793244
  EX_so4_e : 0.107126
  EX_k_e : 0.083036
  EX_fe2_e : 0.006832
  EX_mg2_e : 0.003690
  EX_ca2_e : 0.002214
  EX_cl_e : 0.002214
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.922903
  EX_co2_e : 24.550647
  EX_h_e : 7.367276
  EX_acald_e : 1.732757
  Auxiliary production reaction : 0.691447
  DM_oxam_c : 0.000476
  DM_5drib_c : 0.000285
  EX_glyclt_e : 0.000285
  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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