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 : utp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b3831 b4384 b1278 b3614 b0910 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b3449 b4138 b4123 b0621 b2406 b3918 b0418 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597899 (mmol/gDw/h)
  Minimum Production Rate : 0.315778 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.033245
  EX_o2_e : 279.359559
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.305262
  EX_pi_e : 1.524070
  EX_so4_e : 0.150563
  EX_k_e : 0.116706
  EX_mg2_e : 0.005187
  EX_ca2_e : 0.003112
  EX_cl_e : 0.003112
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990397
  EX_h2o_e : 549.480811
  EX_co2_e : 29.690148
  EX_succ_e : 0.623485
  Auxiliary production reaction : 0.315778
  EX_ura_e : 0.108222
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000133

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.

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Last updated: 21-Sep-2023
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