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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b2836 b3553 b3399 b2744 b3708 b3008 b0871 b0160 b3236 b0120 b1982 b2797 b3117 b1814 b4471 b3449 b1033 b4374 b0675 b2361 b2291 b0261 b3709 b2239 b3161 b0112 b0114 b0886 b0509 b3125 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b1473 b0516 b4141 b1798 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.731536 (mmol/gDw/h)
  Minimum Production Rate : 0.503622 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.759772
  EX_o2_e : 274.377833
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.414721
  EX_pi_e : 2.216568
  EX_so4_e : 0.184215
  EX_k_e : 0.142791
  EX_mg2_e : 0.006346
  EX_ca2_e : 0.003808
  EX_cl_e : 0.003808
  EX_cu2_e : 0.000519
  EX_mn2_e : 0.000505
  EX_zn2_e : 0.000249
  EX_ni2_e : 0.000236
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988251
  EX_h2o_e : 549.789993
  EX_co2_e : 25.436026
  Auxiliary production reaction : 0.503622
  EX_alltn_e : 0.000819
  DM_5drib_c : 0.000491
  DM_4crsol_c : 0.000163
  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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