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 (31 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b0871 b3617 b1982 b1033 b0675 b2361 b2291 b0261 b4388 b4381 b0112 b0114 b0509 b3125 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470339 (mmol/gDw/h)
  Minimum Production Rate : 0.764481 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.756785
  EX_nh4_e : 10.431517
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.982654
  EX_so4_e : 0.118441
  EX_k_e : 0.091807
  EX_fe2_e : 0.007554
  EX_mg2_e : 0.004080
  EX_cl_e : 0.002448
  EX_ca2_e : 0.002448
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.752895
  EX_co2_e : 20.806345
  EX_h_e : 8.145437
  EX_acald_e : 1.915778
  Auxiliary production reaction : 0.764481
  DM_oxam_c : 0.000526
  DM_5drib_c : 0.000316
  EX_glyclt_e : 0.000315
  DM_4crsol_c : 0.000105

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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