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 : ump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b2242 b3553 b1478 b4382 b1241 b3831 b4069 b4384 b3614 b0910 b3752 b3115 b1849 b2296 b2781 b2407 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1779 b1759 b1033 b2799 b3945 b1602 b4138 b4123 b0621 b2406 b3915 b0529 b2492 b0904 b3029 b3028 b1380 b3918 b4042 b2660 b1517 b1206 b0221 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.316978 (mmol/gDw/h)
  Minimum Production Rate : 0.618302 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.246288
  EX_o2_e : 283.295546
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.861455
  EX_pi_e : 0.924060
  EX_so4_e : 0.079821
  EX_k_e : 0.061872
  EX_mg2_e : 0.002750
  EX_ca2_e : 0.001650
  EX_cl_e : 0.001650
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000219
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994909
  EX_h2o_e : 550.257655
  EX_co2_e : 31.229393
  EX_succ_e : 0.828393
  EX_ac_e : 0.741194
  Auxiliary production reaction : 0.618302
  EX_ins_e : 0.497852
  EX_ura_e : 0.105056
  EX_mththf_e : 0.000142
  DM_5drib_c : 0.000071
  DM_4crsol_c : 0.000071

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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