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 : pg140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b2744 b3614 b0910 b4152 b2926 b2781 b1612 b1611 b4122 b1759 b3449 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b2239 b3915 b2197 b3918 b0789 b1249 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.501548 (mmol/gDw/h)
  Minimum Production Rate : 0.264643 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.891045
  EX_o2_e : 273.182008
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.128270
  EX_pi_e : 0.748687
  EX_so4_e : 0.126300
  EX_k_e : 0.097899
  EX_mg2_e : 0.004351
  EX_cl_e : 0.002611
  EX_ca2_e : 0.002611
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991945
  EX_h2o_e : 542.971304
  EX_co2_e : 26.899927
  EX_succ_e : 0.523010
  EX_ura_e : 0.355672
  Auxiliary production reaction : 0.264643
  EX_g3pe_e : 0.000247
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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