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 (60 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3752 b3115 b1849 b2296 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2210 b0411 b2799 b3945 b1602 b3915 b0529 b2492 b0904 b1380 b2660 b1695 b1517 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.407846 (mmol/gDw/h)
  Minimum Production Rate : 0.938605 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.083788
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.726703
  EX_pi_e : 1.332015
  EX_so4_e : 0.102704
  EX_k_e : 0.079609
  EX_fe3_e : 0.006550
  EX_mg2_e : 0.003538
  EX_cl_e : 0.002123
  EX_ca2_e : 0.002123
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 53.552186
  EX_co2_e : 36.264167
  EX_h_e : 6.313445
  Auxiliary production reaction : 0.938605
  EX_ac_e : 0.237442
  EX_ade_e : 0.088959
  DM_mththf_c : 0.088685
  DM_5drib_c : 0.000274
  DM_4crsol_c : 0.000091

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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