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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2242 b3553 b0474 b2518 b2744 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1759 b1033 b4374 b4161 b0675 b1415 b4014 b2976 b4138 b4123 b0621 b2913 b4381 b2406 b0452 b2492 b0904 b2197 b3029 b3028 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.518902 (mmol/gDw/h)
  Minimum Production Rate : 0.273972 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.354631
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.614025
  EX_pi_e : 0.774508
  EX_so4_e : 0.130670
  EX_k_e : 0.101286
  EX_mg2_e : 0.004501
  EX_fe2_e : 0.004282
  EX_fe3_e : 0.004052
  EX_ca2_e : 0.002701
  EX_cl_e : 0.002701
  EX_cu2_e : 0.000368
  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_h2o_e : 48.955082
  EX_co2_e : 31.503485
  EX_h_e : 6.864072
  EX_succ_e : 0.541107
  Auxiliary production reaction : 0.273972
  EX_ura_e : 0.094006
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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