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 : pg180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b4384 b2744 b1278 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b2406 b0452 b2197 b3918 b1206 b3546 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.539160 (mmol/gDw/h)
  Minimum Production Rate : 0.284754 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.432930
  EX_o2_e : 266.993045
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.587567
  EX_pi_e : 0.804831
  EX_so4_e : 0.135771
  EX_k_e : 0.105240
  EX_mg2_e : 0.004677
  EX_ca2_e : 0.002806
  EX_cl_e : 0.002806
  EX_cu2_e : 0.000382
  EX_mn2_e : 0.000373
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991341
  EX_h2o_e : 539.408829
  EX_co2_e : 22.131982
  EX_succ_e : 0.562231
  EX_ura_e : 0.382344
  Auxiliary production reaction : 0.284754
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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.

Last updated: 21-Sep-2023
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