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 : pg161_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b4069 b2744 b1278 b3614 b0910 b4152 b2297 b2458 b2781 b1612 b1611 b4122 b1759 b3616 b3589 b4374 b0675 b4388 b4138 b4123 b0621 b4381 b2406 b0452 b0529 b2197 b3918 b1206 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458179 (mmol/gDw/h)
  Minimum Production Rate : 0.241985 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.031534
  EX_o2_e : 272.371006
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.598122
  EX_pi_e : 0.683946
  EX_so4_e : 0.115379
  EX_k_e : 0.089433
  EX_mg2_e : 0.003975
  EX_ca2_e : 0.002385
  EX_cl_e : 0.002385
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992641
  EX_h2o_e : 541.177982
  EX_co2_e : 26.012127
  EX_ac_e : 1.387762
  EX_succ_e : 0.477785
  EX_ura_e : 0.324916
  Auxiliary production reaction : 0.241985
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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