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 (101 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3831 b2744 b3614 b0910 b3752 b3926 b4152 b2926 b2781 b1612 b1611 b4122 b1759 b2440 b4374 b2361 b2291 b0411 b3945 b4138 b4123 b0621 b0452 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.519751 (mmol/gDw/h)
  Minimum Production Rate : 0.274420 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.943663
  EX_o2_e : 281.718042
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.350433
  EX_pi_e : 1.050196
  EX_so4_e : 0.130884
  EX_k_e : 0.101452
  EX_mg2_e : 0.004509
  EX_ca2_e : 0.002705
  EX_cl_e : 0.002705
  EX_cu2_e : 0.000369
  EX_mn2_e : 0.000359
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991652
  EX_h2o_e : 549.209025
  EX_co2_e : 32.005422
  EX_succ_e : 0.541993
  Auxiliary production reaction : 0.274420
  EX_ura_e : 0.094160
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116
  EX_glyald_e : 0.000084

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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