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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b3617 b0030 b2883 b1982 b2797 b3117 b1814 b4471 b1033 b0595 b1623 b0261 b0507 b3709 b4381 b2406 b3161 b0112 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3821 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437111 (mmol/gDw/h)
  Minimum Production Rate : 0.654001 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.390635
  EX_o2_e : 269.488816
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.299262
  EX_pi_e : 2.383644
  EX_so4_e : 0.764075
  EX_k_e : 0.085321
  EX_mg2_e : 0.003792
  EX_ca2_e : 0.002275
  EX_cl_e : 0.002275
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992980
  EX_h2o_e : 545.696985
  EX_co2_e : 20.422593
  EX_ac_e : 2.968717
  Auxiliary production reaction : 0.654001
  DM_oxam_c : 0.000489
  DM_5drib_c : 0.000293
  EX_glyclt_e : 0.000292
  DM_4crsol_c : 0.000097

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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