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 : pe120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2242 b3553 b4382 b3831 b4384 b3614 b0910 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4138 b4123 b0621 b2406 b0306 b3605 b2492 b0904 b2197 b3028 b3821 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.490364 (mmol/gDw/h)
  Minimum Production Rate : 0.258655 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.027604
  EX_o2_e : 275.819964
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.249365
  EX_pi_e : 0.731663
  EX_so4_e : 0.123483
  EX_k_e : 0.095716
  EX_mg2_e : 0.004254
  EX_cl_e : 0.002552
  EX_ca2_e : 0.002552
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992124
  EX_h2o_e : 544.906375
  EX_co2_e : 28.936792
  EX_succ_e : 0.511347
  EX_ura_e : 0.347412
  Auxiliary production reaction : 0.258655
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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