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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b3709 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.713617 (mmol/gDw/h)
  Minimum Production Rate : 0.180179 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.366610
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.971049
  EX_pi_e : 1.228898
  EX_so4_e : 0.359883
  EX_k_e : 0.139293
  EX_fe2_e : 0.011461
  EX_mg2_e : 0.006191
  EX_ca2_e : 0.003714
  EX_cl_e : 0.003714
  EX_cu2_e : 0.000506
  EX_mn2_e : 0.000493
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.618500
  EX_co2_e : 25.158715
  EX_h_e : 7.700737
  EX_ac_e : 0.595637
  Auxiliary production reaction : 0.180179
  DM_oxam_c : 0.002786
  DM_5drib_c : 0.002466
  DM_4crsol_c : 0.002147
  EX_glyclt_e : 0.001987

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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