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 (79 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b0160 b3844 b1004 b3713 b1109 b0046 b1779 b2463 b0937 b1982 b3616 b3589 b2210 b4374 b0675 b2361 b2291 b3551 b0261 b3945 b1602 b4219 b1832 b1778 b1727 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.334303 (mmol/gDw/h)
  Minimum Production Rate : 0.514003 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.334893
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.386543
  EX_pi_e : 1.350477
  EX_so4_e : 0.084184
  EX_k_e : 0.065254
  EX_fe2_e : 0.005369
  EX_mg2_e : 0.002900
  EX_ca2_e : 0.001740
  EX_cl_e : 0.001740
  EX_cu2_e : 0.000237
  EX_mn2_e : 0.000231
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 51.653934
  EX_co2_e : 33.512232
  EX_h_e : 5.819802
  EX_etoh_e : 0.808531
  Auxiliary production reaction : 0.514003
  EX_his__L_e : 0.058735
  EX_ade_e : 0.000374
  DM_5drib_c : 0.000224
  DM_4crsol_c : 0.000075

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.

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Last updated: 21-Sep-2023
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