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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b3399 b0474 b2518 b1241 b0351 b2744 b0871 b2925 b2097 b0160 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b3946 b2210 b0825 b0675 b2361 b4015 b0261 b2799 b3945 b1602 b2913 b4381 b3915 b0452 b1727 b0529 b2492 b0904 b3927 b1380 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361772 (mmol/gDw/h)
  Minimum Production Rate : 0.047117 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.007620
  EX_o2_e : 280.458915
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.097125
  EX_pi_e : 0.396066
  EX_so4_e : 0.091102
  EX_k_e : 0.070615
  EX_mg2_e : 0.003138
  EX_ca2_e : 0.001883
  EX_cl_e : 0.001883
  EX_cu2_e : 0.000256
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994188
  EX_h2o_e : 543.851526
  EX_co2_e : 28.401048
  EX_pyr_e : 5.378248
  Auxiliary production reaction : 0.047099
  EX_hxan_e : 0.000405
  DM_5drib_c : 0.000243
  DM_4crsol_c : 0.000081

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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