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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b0160 b2797 b3117 b1814 b4471 b3616 b3589 b1623 b3665 b0675 b2361 b4381 b2406 b0112 b0452 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b0594 b4141 b1798 b1517 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510010 (mmol/gDw/h)
  Minimum Production Rate : 0.401133 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.503166
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.315992
  EX_pi_e : 1.695357
  EX_so4_e : 0.529564
  EX_k_e : 0.099550
  EX_fe3_e : 0.008191
  EX_mg2_e : 0.004424
  EX_ca2_e : 0.002655
  EX_cl_e : 0.002655
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.136025
  EX_co2_e : 22.841584
  EX_h_e : 5.897762
  EX_acald_e : 1.693732
  Auxiliary production reaction : 0.401133
  DM_mththf_c : 0.000228
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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