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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b2836 b1478 b1241 b4069 b4384 b2744 b3708 b3008 b0910 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2926 b0030 b1238 b2883 b2690 b1982 b2688 b2797 b3117 b1814 b4471 b0675 b4014 b0261 b2976 b0822 b0335 b3709 b4381 b2406 b3161 b0112 b2868 b4064 b4464 b2975 b0114 b3603 b0728 b0509 b3125 b0529 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b0508 b1473 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532324 (mmol/gDw/h)
  Minimum Production Rate : 0.091149 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.757722
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.252204
  EX_pi_e : 0.695781
  EX_so4_e : 0.360776
  EX_k_e : 0.103906
  EX_fe2_e : 0.008550
  EX_mg2_e : 0.004618
  EX_ca2_e : 0.002771
  EX_cl_e : 0.002771
  EX_cu2_e : 0.000377
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.714034
  EX_co2_e : 29.192140
  EX_h_e : 5.386392
  EX_ac_e : 0.536638
  EX_cys__L_e : 0.226726
  Auxiliary production reaction : 0.091149
  EX_ade_e : 0.000596
  DM_5drib_c : 0.000357
  DM_4crsol_c : 0.000119

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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