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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3617 b2407 b3124 b1982 b1033 b0261 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461255 (mmol/gDw/h)
  Minimum Production Rate : 0.883983 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.052560
  EX_nh4_e : 11.169911
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.096878
  EX_so4_e : 0.116153
  EX_k_e : 0.090034
  EX_fe2_e : 0.007408
  EX_mg2_e : 0.004001
  EX_ca2_e : 0.002401
  EX_cl_e : 0.002401
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.013237
  EX_co2_e : 19.384113
  EX_h_e : 9.334053
  EX_ac_e : 1.558586
  Auxiliary production reaction : 0.883983
  DM_oxam_c : 0.000516
  DM_5drib_c : 0.000310
  EX_glyclt_e : 0.000309
  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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