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 (65 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b1623 b3665 b2799 b3945 b1602 b4381 b2406 b3915 b3654 b3714 b3664 b0529 b2492 b0904 b1380 b2660 b1511 b0606 b0221 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400442 (mmol/gDw/h)
  Minimum Production Rate : 1.237752 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.278162
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.842156
  EX_pi_e : 1.624021
  EX_so4_e : 0.100839
  EX_k_e : 0.078163
  EX_fe3_e : 0.006432
  EX_mg2_e : 0.003474
  EX_ca2_e : 0.002084
  EX_cl_e : 0.002084
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 53.538623
  EX_co2_e : 35.446457
  EX_h_e : 6.521987
  Auxiliary production reaction : 1.237752
  EX_ac_e : 0.233132
  EX_glyclt_e : 0.085587
  EX_hxan_e : 0.010478
  DM_mththf_c : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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