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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0586 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b1238 b3124 b1982 b2688 b2797 b3117 b1814 b4471 b2440 b0261 b4381 b2406 b2789 b3127 b0452 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.709945 (mmol/gDw/h)
  Minimum Production Rate : 0.141012 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.004174
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.978228
  EX_pi_e : 0.684817
  EX_so4_e : 0.178778
  EX_k_e : 0.138576
  EX_fe2_e : 0.011402
  EX_mg2_e : 0.006159
  EX_ca2_e : 0.003695
  EX_cl_e : 0.003695
  EX_cu2_e : 0.000503
  EX_mn2_e : 0.000491
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 45.762110
  EX_co2_e : 25.602715
  EX_h_e : 7.643227
  EX_ac_e : 0.413320
  DM_oxam_c : 0.282817
  DM_5drib_c : 0.282499
  DM_4crsol_c : 0.282181
  Auxiliary production reaction : 0.141012
  EX_etha_e : 0.028062

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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