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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b4467 b3399 b1241 b0351 b2744 b3708 b3008 b0871 b2779 b0160 b1004 b3713 b1109 b0046 b3124 b3236 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b3709 b3161 b0112 b2789 b3127 b3915 b0452 b1727 b2975 b3603 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b1473 b1600 b2660 b0514 b4141 b1798 b1985 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481082 (mmol/gDw/h)
  Minimum Production Rate : 0.021767 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.596214
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.458904
  EX_pi_e : 0.464054
  EX_so4_e : 0.121147
  EX_k_e : 0.093904
  EX_fe3_e : 0.029488
  EX_mg2_e : 0.004173
  EX_ca2_e : 0.002504
  EX_cl_e : 0.002504
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.378443
  EX_co2_e : 38.748663
  EX_h_e : 4.800158
  EX_hxan_e : 0.044057
  DM_5drib_c : 0.043841
  Auxiliary production reaction : 0.021759
  DM_4crsol_c : 0.000107

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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