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 : cpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2925 b2097 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b0261 b3945 b4381 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.773680 (mmol/gDw/h)
  Minimum Production Rate : 0.157343 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.968877
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.163497
  EX_pi_e : 0.903639
  EX_so4_e : 0.194828
  EX_k_e : 0.151017
  EX_fe2_e : 0.012426
  EX_mg2_e : 0.006712
  EX_ca2_e : 0.004027
  EX_cl_e : 0.004027
  EX_cu2_e : 0.000549
  EX_mn2_e : 0.000535
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.579522
  EX_co2_e : 26.014359
  EX_h_e : 7.984559
  EX_pyr_e : 0.204092
  Auxiliary production reaction : 0.157343
  DM_oxam_c : 0.021110
  DM_5drib_c : 0.000519
  DM_4crsol_c : 0.000173

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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