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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (118 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 65
  Gene deletion: b4467 b2836 b2242 b3399 b0469 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b3614 b0910 b2297 b2458 b2779 b2781 b1612 b1611 b4122 b1779 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0596 b3665 b4374 b0675 b2361 b2291 b1415 b1014 b2799 b3945 b1907 b4138 b4123 b0621 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b3927 b3028 b1380 b3918 b1912 b1473 b4266 b2842 b1813 b1206 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.317602 (mmol/gDw/h)
  Minimum Production Rate : 0.526851 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.396912
  EX_o2_e : 282.759562
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.184276
  EX_pi_e : 1.360064
  EX_so4_e : 0.079979
  EX_k_e : 0.061994
  EX_mg2_e : 0.002755
  EX_ca2_e : 0.001653
  EX_cl_e : 0.001653
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000219
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994899
  EX_h2o_e : 548.836523
  EX_co2_e : 31.286533
  EX_ac_e : 1.048220
  EX_succ_e : 0.965401
  Auxiliary production reaction : 0.526851
  EX_ade_e : 0.317104
  EX_ura_e : 0.057487
  EX_dxylnt_e : 0.000212
  DM_5drib_c : 0.000071
  DM_4crsol_c : 0.000071

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.

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Last updated: 21-Sep-2023
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