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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3708 b3008 b0871 b2779 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b1539 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488066 (mmol/gDw/h)
  Minimum Production Rate : 0.108305 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.809802
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.298538
  EX_pi_e : 0.470791
  EX_so4_e : 0.122905
  EX_k_e : 0.095267
  EX_fe2_e : 0.007839
  EX_mg2_e : 0.004234
  EX_cl_e : 0.002540
  EX_ca2_e : 0.002540
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.449859
  EX_co2_e : 38.277072
  EX_h_e : 5.512012
  EX_hxan_e : 0.121076
  Auxiliary production reaction : 0.108305
  EX_ade_e : 0.000328
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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