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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3831 b3614 b0910 b3752 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b2690 b1759 b3449 b0411 b3945 b4138 b4123 b0621 b2913 b4381 b0529 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.711197 (mmol/gDw/h)
  Minimum Production Rate : 0.009156 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.961873
  EX_o2_e : 274.845512
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.689549
  EX_pi_e : 0.686024
  EX_so4_e : 0.179094
  EX_k_e : 0.138821
  EX_mg2_e : 0.006170
  EX_ca2_e : 0.003702
  EX_cl_e : 0.003702
  EX_cu2_e : 0.000504
  EX_mn2_e : 0.000491
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988577
  EX_h2o_e : 547.533495
  EX_co2_e : 25.394404
  EX_succ_e : 0.741630
  EX_ura_e : 0.504344
  Auxiliary production reaction : 0.009156
  DM_5drib_c : 0.000160
  DM_4crsol_c : 0.000159

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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