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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3831 b2744 b3614 b0910 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b0411 b4138 b4123 b0621 b3736 b2197 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.238911 (mmol/gDw/h)
  Minimum Production Rate : 0.252321 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 982.252439
  EX_o2_e : 265.179851
  EX_glc__D_e : 10.000000
  EX_nh4_e : 2.919069
  EX_pi_e : 0.230455
  EX_so4_e : 0.060163
  EX_k_e : 0.046634
  EX_mg2_e : 0.002073
  EX_ca2_e : 0.001244
  EX_cl_e : 0.001244
  EX_cu2_e : 0.000169
  EX_mn2_e : 0.000165
  EX_zn2_e : 0.000081
  EX_ni2_e : 0.000077

Product: (mmol/gDw/h)
  EX_fe3_e : 999.996163
  EX_h2o_e : 523.976875
  EX_co2_e : 16.573555
  EX_ac_e : 14.459074
  Auxiliary production reaction : 0.252321
  EX_succ_e : 0.249135
  EX_ura_e : 0.169423
  DM_5drib_c : 0.000054
  DM_4crsol_c : 0.000053

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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