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 : pgp160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b2242 b3553 b4382 b3846 b2341 b0474 b2518 b3831 b4384 b1278 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4161 b1415 b4138 b4123 b0621 b2406 b2492 b0904 b2197 b3028 b3918 b1206 b3546 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453573 (mmol/gDw/h)
  Minimum Production Rate : 0.239552 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.259149
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.541849
  EX_pi_e : 0.916624
  EX_so4_e : 0.114219
  EX_k_e : 0.088534
  EX_fe2_e : 0.007285
  EX_mg2_e : 0.003935
  EX_ca2_e : 0.002361
  EX_cl_e : 0.002361
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.878897
  EX_co2_e : 29.101400
  EX_h_e : 5.517322
  EX_succ_e : 0.472982
  EX_ura_e : 0.321650
  Auxiliary production reaction : 0.239552
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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