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 : pe120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (104 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b2242 b3553 b0474 b2518 b3831 b2744 b2925 b2097 b2781 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0651 b2162 b2690 b1759 b2210 b1033 b4374 b4161 b2361 b2291 b1415 b0411 b3945 b4138 b4123 b0621 b0452 b2492 b0904 b2197 b3825 b3028 b3918 b1912 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491676 (mmol/gDw/h)
  Minimum Production Rate : 0.152923 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.452072
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.160326
  EX_fe3_e : 2.138111
  EX_pi_e : 0.627197
  EX_so4_e : 0.123814
  EX_k_e : 0.095972
  EX_mg2_e : 0.004265
  EX_cl_e : 0.002559
  EX_ca2_e : 0.002559
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.568229
  EX_co2_e : 31.938636
  EX_h_e : 8.225678
  EX_fe2_e : 2.130214
  EX_succ_e : 0.512716
  EX_ura_e : 0.348671
  Auxiliary production reaction : 0.152923
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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