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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b0474 b2518 b1241 b0351 b2744 b4152 b2297 b2458 b2926 b2781 b3617 b1612 b1611 b4122 b1759 b2440 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b2913 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442124 (mmol/gDw/h)
  Minimum Production Rate : 0.233505 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.943325
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.401958
  EX_pi_e : 0.893486
  EX_so4_e : 0.111336
  EX_k_e : 0.086299
  EX_fe2_e : 0.007101
  EX_mg2_e : 0.003835
  EX_ca2_e : 0.002301
  EX_cl_e : 0.002301
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.823986
  EX_co2_e : 36.186007
  EX_h_e : 5.144544
  EX_succ_e : 0.461043
  Auxiliary production reaction : 0.233505
  EX_ura_e : 0.080026
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000099

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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