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 : uamr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 39: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b2242 b0474 b2518 b2744 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0306 b3605 b2197 b3028 b3821 b3918 b0789 b1249 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.540657 (mmol/gDw/h)
  Minimum Production Rate : 0.285545 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.153558
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.891408
  EX_pi_e : 1.092612
  EX_so4_e : 0.136148
  EX_k_e : 0.105532
  EX_fe2_e : 0.008683
  EX_mg2_e : 0.004690
  EX_ca2_e : 0.002814
  EX_cl_e : 0.002814
  EX_cu2_e : 0.000383
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.206562
  EX_co2_e : 29.449663
  EX_h_e : 6.863497
  EX_succ_e : 0.563793
  Auxiliary production reaction : 0.285545
  EX_ura_e : 0.097861
  EX_for_e : 0.001326
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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