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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b2926 b1850 b0030 b2407 b1982 b3616 b3589 b3665 b2406 b0112 b0114 b0529 b2492 b0904 b1380 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.523078 (mmol/gDw/h)
  Minimum Production Rate : 1.701101 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.905049
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.053157
  EX_pi_e : 2.205665
  EX_so4_e : 0.131721
  EX_k_e : 0.102101
  EX_fe2_e : 0.008401
  EX_mg2_e : 0.004538
  EX_ca2_e : 0.002723
  EX_cl_e : 0.002723
  EX_cu2_e : 0.000371
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.423170
  EX_co2_e : 27.400006
  EX_h_e : 8.210209
  Auxiliary production reaction : 1.701101
  EX_acald_e : 0.460259
  EX_ade_e : 0.000352
  DM_mththf_c : 0.000234
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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