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 : cpe180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b2242 b2744 b1278 b3614 b0910 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b4374 b0675 b2361 b2291 b1415 b4014 b2976 b4138 b4123 b0621 b2197 b3028 b3821 b3918 b1206 b3546 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446321 (mmol/gDw/h)
  Minimum Production Rate : 0.235722 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.563727
  EX_o2_e : 274.162775
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.688963
  EX_pi_e : 0.666246
  EX_so4_e : 0.112392
  EX_k_e : 0.087119
  EX_mg2_e : 0.003872
  EX_ca2_e : 0.002323
  EX_cl_e : 0.002323
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992832
  EX_h2o_e : 543.425907
  EX_co2_e : 28.416828
  EX_succ_e : 0.465420
  EX_ura_e : 0.316507
  Auxiliary production reaction : 0.235722
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000100

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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