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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b3942 b1732 b4069 b2744 b3708 b3008 b2297 b2458 b2925 b2097 b0160 b1238 b3124 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0675 b2361 b0261 b4381 b2406 b2943 b0114 b2366 b2492 b0904 b2947 b2578 b1533 b3927 b2835 b0494 b0594 b0514 b0516   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.706241 (mmol/gDw/h)
  Minimum Production Rate : 0.134705 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.705861
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.151520
  EX_pi_e : 0.815949
  EX_so4_e : 0.556286
  EX_k_e : 0.137853
  EX_fe2_e : 0.011343
  EX_mg2_e : 0.006127
  EX_cl_e : 0.003676
  EX_ca2_e : 0.003676
  EX_cu2_e : 0.000501
  EX_mn2_e : 0.000488
  EX_zn2_e : 0.000241
  EX_ni2_e : 0.000228
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 46.125205
  EX_co2_e : 26.289128
  EX_h_e : 7.181813
  EX_ac_e : 0.789604
  EX_met__L_e : 0.378440
  Auxiliary production reaction : 0.134705
  EX_alltn_e : 0.002757
  DM_5drib_c : 0.002441
  DM_4crsol_c : 0.002124
  EX_glyc__R_e : 0.000983

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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