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 : cdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 63
  Gene deletion: b2836 b2242 b3553 b3399 b1241 b0351 b4069 b2744 b3708 b3614 b0910 b2297 b2458 b2926 b2781 b0160 b1612 b1611 b4122 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0595 b1623 b3665 b4374 b0675 b2361 b2291 b1415 b1014 b0822 b2799 b3709 b1907 b4138 b4123 b0621 b3161 b0112 b0114 b2366 b2492 b0904 b1533 b3028 b1380 b3918 b1912 b1473 b4266 b2842 b1517 b1206 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.293842 (mmol/gDw/h)
  Minimum Production Rate : 0.780752 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.937629
  EX_o2_e : 283.834990
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.822292
  EX_pi_e : 1.844946
  EX_so4_e : 0.073995
  EX_k_e : 0.057356
  EX_mg2_e : 0.002549
  EX_ca2_e : 0.001529
  EX_cl_e : 0.001529
  EX_cu2_e : 0.000208
  EX_mn2_e : 0.000203
  EX_zn2_e : 0.000100
  EX_ni2_e : 0.000095

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995281
  EX_h2o_e : 552.155666
  EX_co2_e : 31.518887
  EX_succ_e : 1.186493
  EX_ac_e : 1.116459
  Auxiliary production reaction : 0.780752
  EX_ade_e : 0.440038
  EX_ura_e : 0.053186
  EX_dxylnt_e : 0.000197
  DM_mththf_c : 0.000132
  DM_5drib_c : 0.000066
  DM_4crsol_c : 0.000066

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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