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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3708 b2297 b2458 b2779 b0030 b2407 b1238 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b1982 b1302 b2662 b4139 b2797 b3117 b1814 b4471 b1623 b4014 b0261 b2976 b2799 b3945 b1602 b2913 b4381 b2406 b2789 b3127 b3915 b2975 b3603 b1539 b2492 b0904 b2954 b1533 b3029 b1380 b1600 b0514 b4141 b1798 b3662 b0221 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492368 (mmol/gDw/h)
  Minimum Production Rate : 0.005715 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.965356
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.364676
  EX_pi_e : 0.474941
  EX_so4_e : 0.123989
  EX_k_e : 0.096107
  EX_fe3_e : 0.007910
  EX_mg2_e : 0.004271
  EX_ca2_e : 0.002563
  EX_cl_e : 0.002563
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.149073
  EX_co2_e : 39.005557
  EX_h_e : 4.871395
  EX_ac_e : 0.286651
  EX_hxan_e : 0.011785
  DM_5drib_c : 0.011564
  DM_4crsol_c : 0.011344
  Auxiliary production reaction : 0.005617

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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