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 : pe141_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b2744 b3614 b0910 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b2440 b4374 b0675 b4138 b4123 b0621 b0153 b4381 b2406 b3453 b0591 b2197 b3918 b1912 b2240 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.580291 (mmol/gDw/h)
  Minimum Production Rate : 0.306431 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.931947
  EX_o2_e : 268.004679
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.396591
  EX_pi_e : 0.866229
  EX_so4_e : 0.146129
  EX_k_e : 0.113269
  EX_mg2_e : 0.005034
  EX_ca2_e : 0.003020
  EX_cl_e : 0.003020
  EX_cu2_e : 0.000411
  EX_mn2_e : 0.000401
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990680
  EX_h2o_e : 541.516842
  EX_co2_e : 22.002749
  EX_succ_e : 0.605122
  EX_ura_e : 0.411512
  Auxiliary production reaction : 0.306431
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000129
  EX_g3pe_e : 0.000047

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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