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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b1479 b3752 b0871 b3617 b2407 b3844 b3236 b2463 b1982 b2210 b3551 b4219 b1832 b1778 b2406 b2868 b0114 b0529 b2492 b0904 b1710 b2480 b3662 b1517 b0606   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.528316 (mmol/gDw/h)
  Minimum Production Rate : 0.859069 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.629550
  EX_nh4_e : 10.002891
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.368686
  EX_so4_e : 0.133041
  EX_k_e : 0.103124
  EX_fe2_e : 0.008485
  EX_mg2_e : 0.004583
  EX_ca2_e : 0.002750
  EX_cl_e : 0.002750
  EX_cu2_e : 0.000375
  EX_mn2_e : 0.000365
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.801855
  EX_co2_e : 18.002685
  EX_h_e : 13.686921
  EX_fum_e : 1.408641
  EX_acald_e : 1.323937
  Auxiliary production reaction : 0.859069
  EX_ade_e : 0.000356
  DM_mththf_c : 0.000237
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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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