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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3399 b4382 b2502 b4384 b2744 b3708 b3008 b0871 b2407 b3124 b0517 b0121 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b0261 b3709 b2239 b2406 b3161 b0112 b2789 b3127 b0452 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b0594 b0514 b4141 b1798 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.735483 (mmol/gDw/h)
  Minimum Production Rate : 0.506340 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.187109
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.465530
  EX_pi_e : 1.722191
  EX_so4_e : 0.185209
  EX_k_e : 0.143561
  EX_mg2_e : 0.006380
  EX_fe2_e : 0.006070
  EX_fe3_e : 0.005743
  EX_cl_e : 0.003828
  EX_ca2_e : 0.003828
  EX_cu2_e : 0.000521
  EX_mn2_e : 0.000508
  EX_zn2_e : 0.000251
  EX_ni2_e : 0.000238
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 49.231588
  EX_co2_e : 25.249495
  EX_h_e : 7.779571
  Auxiliary production reaction : 0.506340
  EX_alltn_e : 0.000823
  DM_5drib_c : 0.000494
  DM_4crsol_c : 0.000164
  EX_g3pe_e : 0.000059

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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