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 : utp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b2242 b3831 b3614 b0910 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1415 b4138 b4123 b0621 b4381 b2406 b0452 b3028 b3918 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.567651 (mmol/gDw/h)
  Minimum Production Rate : 0.299802 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.911258
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.935685
  EX_pi_e : 1.446967
  EX_so4_e : 0.142946
  EX_k_e : 0.110802
  EX_fe2_e : 0.009117
  EX_mg2_e : 0.004924
  EX_ca2_e : 0.002955
  EX_cl_e : 0.002955
  EX_cu2_e : 0.000402
  EX_mn2_e : 0.000392
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.016148
  EX_co2_e : 31.222147
  EX_h_e : 6.606578
  EX_succ_e : 0.591942
  Auxiliary production reaction : 0.299802
  EX_ura_e : 0.102747
  EX_for_e : 0.001392
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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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