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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4069 b4384 b2744 b3708 b3008 b2297 b2458 b2925 b2097 b0030 b2883 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b3945 b0507 b4381 b0112 b0452 b2868 b4064 b4464 b2975 b0114 b3603 b0529 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.585088 (mmol/gDw/h)
  Minimum Production Rate : 0.247842 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.832888
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.057072
  EX_pi_e : 1.060064
  EX_so4_e : 0.147337
  EX_k_e : 0.114205
  EX_fe2_e : 0.009397
  EX_mg2_e : 0.005076
  EX_ca2_e : 0.003045
  EX_cl_e : 0.003045
  EX_cu2_e : 0.000415
  EX_mn2_e : 0.000404
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.998241
  EX_co2_e : 27.336446
  EX_h_e : 8.090219
  EX_ac_e : 1.719552
  Auxiliary production reaction : 0.247842
  EX_ade_e : 0.000655
  DM_5drib_c : 0.000393
  DM_4crsol_c : 0.000130

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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