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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3399 b3942 b1732 b1241 b0351 b4069 b2744 b3926 b0871 b2297 b2458 b2779 b2925 b2097 b0160 b3844 b1004 b3713 b1109 b0046 b0907 b2690 b1982 b3616 b3589 b2210 b1033 b0675 b2361 b3945 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.278190 (mmol/gDw/h)
  Minimum Production Rate : 1.052102 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.945312
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.190598
  EX_pi_e : 2.372547
  EX_so4_e : 0.070054
  EX_k_e : 0.054301
  EX_fe2_e : 0.004468
  EX_mg2_e : 0.002413
  EX_ca2_e : 0.001448
  EX_cl_e : 0.001448
  EX_cu2_e : 0.000197
  EX_mn2_e : 0.000192
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 47.128824
  EX_co2_e : 26.682591
  EX_h_e : 9.104272
  EX_pyr_e : 3.563892
  Auxiliary production reaction : 1.052102
  EX_ac_e : 0.850129
  EX_xan_e : 0.007279
  EX_hxan_e : 0.000187
  DM_mththf_c : 0.000125
  DM_5drib_c : 0.000063
  EX_glyc__R_e : 0.000062
  DM_4crsol_c : 0.000062

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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