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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b4069 b2744 b3708 b2297 b2458 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b3236 b2883 b2690 b2797 b3117 b1814 b4471 b3449 b0261 b1602 b2913 b4381 b2406 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b0494 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421269 (mmol/gDw/h)
  Minimum Production Rate : 0.268380 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 39.574846
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.891573
  EX_pi_e : 0.674739
  EX_so4_e : 0.106084
  EX_k_e : 0.082229
  EX_fe2_e : 0.006766
  EX_mg2_e : 0.003655
  EX_cl_e : 0.002193
  EX_ca2_e : 0.002193
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.879633
  EX_co2_e : 39.802893
  EX_h_e : 5.457948
  Auxiliary production reaction : 0.268380
  EX_ac_e : 0.245257
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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