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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b0238 b0125 b1241 b4069 b2744 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b0477 b4374 b2361 b2291 b2799 b3945 b1602 b3915 b0529 b2492 b0904 b2954 b1380 b2660 b1695 b1518 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449596 (mmol/gDw/h)
  Minimum Production Rate : 0.344896 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.711157
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.627448
  EX_pi_e : 0.778579
  EX_so4_e : 0.113217
  EX_k_e : 0.087758
  EX_fe3_e : 0.007221
  EX_mg2_e : 0.003900
  EX_cl_e : 0.002340
  EX_ca2_e : 0.002340
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.593090
  EX_co2_e : 36.737453
  EX_h_e : 6.171886
  EX_hxan_e : 0.442962
  Auxiliary production reaction : 0.344896
  EX_ac_e : 0.261749
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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