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 : uacmamu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2744 b3614 b0910 b4152 b2297 b2458 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b2690 b1759 b4374 b0675 b4015 b3945 b4388 b4138 b4123 b0621 b4381 b0529 b2197 b3918 b1912 b1206 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.383328 (mmol/gDw/h)
  Minimum Production Rate : 0.202453 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.204871
  EX_o2_e : 281.091160
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.886036
  EX_pi_e : 0.774666
  EX_so4_e : 0.096530
  EX_k_e : 0.074823
  EX_mg2_e : 0.003325
  EX_ca2_e : 0.001995
  EX_cl_e : 0.001995
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993843
  EX_h2o_e : 544.396294
  EX_co2_e : 31.100656
  EX_ac_e : 3.923666
  EX_succ_e : 0.399731
  Auxiliary production reaction : 0.202453
  EX_ura_e : 0.069384
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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