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 (102 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b0474 b2518 b4384 b2744 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b1759 b0477 b1200 b4374 b4161 b0675 b4138 b4123 b0621 b2406 b0114 b2492 b0904 b3825 b3918 b1912 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.684513 (mmol/gDw/h)
  Minimum Production Rate : 0.361522 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.024022
  EX_o2_e : 272.751768
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.363523
  EX_pi_e : 1.383329
  EX_so4_e : 0.172374
  EX_k_e : 0.133612
  EX_mg2_e : 0.005938
  EX_ca2_e : 0.003563
  EX_cl_e : 0.003563
  EX_cu2_e : 0.000485
  EX_mn2_e : 0.000473
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989006
  EX_h2o_e : 545.787840
  EX_co2_e : 23.130247
  EX_succ_e : 0.713805
  Auxiliary production reaction : 0.361522
  EX_ura_e : 0.123899
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000153

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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