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 : hdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 80: 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 b3844 b1612 b1611 b4122 b0651 b2162 b1759 b4138 b4123 b0621 b2406 b3736 b0452 b2197 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.243548 (mmol/gDw/h)
  Minimum Production Rate : 0.128589 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 981.910187
  EX_o2_e : 265.472272
  EX_glc__D_e : 10.000000
  EX_nh4_e : 2.975718
  EX_pi_e : 0.234928
  EX_so4_e : 0.061330
  EX_k_e : 0.047539
  EX_mg2_e : 0.002113
  EX_ca2_e : 0.001268
  EX_cl_e : 0.001268
  EX_cu2_e : 0.000173
  EX_mn2_e : 0.000168
  EX_zn2_e : 0.000083
  EX_ni2_e : 0.000079

Product: (mmol/gDw/h)
  EX_fe3_e : 999.996088
  EX_h2o_e : 524.054053
  EX_co2_e : 16.507059
  EX_ac_e : 14.866136
  EX_succ_e : 0.253970
  EX_ura_e : 0.172711
  Auxiliary production reaction : 0.128589
  DM_5drib_c : 0.000055
  DM_4crsol_c : 0.000054

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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