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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (113 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b3617 b1004 b3713 b1109 b0046 b3236 b2690 b1302 b2662 b2210 b1033 b0675 b4015 b0822 b1602 b1727 b1380 b2660 b1771 b0606 b0221 b2285 b3893 b1474 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.407616 (mmol/gDw/h)
  Minimum Production Rate : 1.196316 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.004320
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.402217
  EX_pi_e : 0.393189
  EX_so4_e : 0.102646
  EX_k_e : 0.079564
  EX_mg2_e : 0.003536
  EX_fe2_e : 0.003364
  EX_fe3_e : 0.003183
  EX_ca2_e : 0.002122
  EX_cl_e : 0.002122
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 43.668156
  EX_co2_e : 28.922269
  EX_h_e : 9.891243
  EX_pyr_e : 3.983470
  EX_for_e : 1.921944
  EX_ac_e : 0.237308
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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