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 : cdpdtdec7eg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b2836 b2242 b0474 b2518 b2744 b1278 b2779 b2781 b3844 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1779 b1759 b2210 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b3915 b3453 b0529 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b2240 b0418 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369140 (mmol/gDw/h)
  Minimum Production Rate : 0.194633 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.503229
  EX_o2_e : 282.810956
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.704864
  EX_pi_e : 0.745667
  EX_so4_e : 0.092957
  EX_k_e : 0.072054
  EX_mg2_e : 0.003202
  EX_ca2_e : 0.001921
  EX_cl_e : 0.001921
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994071
  EX_h2o_e : 548.249263
  EX_co2_e : 35.253383
  EX_succ_e : 0.384936
  Auxiliary production reaction : 0.194633
  EX_ura_e : 0.067142
  EX_glyc3p_e : 0.000326
  EX_glyclt_e : 0.000247
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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