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 : ahdt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b3399 b4069 b2744 b3708 b3926 b0512 b2297 b2458 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b1701 b1805 b1602 b2913 b4381 b2406 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462343 (mmol/gDw/h)
  Minimum Production Rate : 0.275624 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.597882
  EX_o2_e : 287.671878
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.421845
  EX_pi_e : 1.272851
  EX_so4_e : 0.116427
  EX_k_e : 0.090246
  EX_mg2_e : 0.004011
  EX_ca2_e : 0.002406
  EX_cl_e : 0.002406
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992574
  EX_h2o_e : 553.842021
  EX_co2_e : 37.939888
  Auxiliary production reaction : 0.275624
  EX_ac_e : 0.269170
  EX_hxan_e : 0.012615
  DM_5drib_c : 0.000310
  DM_4crsol_c : 0.000103

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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