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 : uamr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 39: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b2242 b3831 b3614 b0910 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1415 b1701 b1805 b4138 b4123 b0621 b4381 b2406 b2197 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 : 0.540659 (mmol/gDw/h)
  Minimum Production Rate : 0.285546 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.127795
  EX_o2_e : 279.151278
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.891432
  EX_pi_e : 1.092616
  EX_so4_e : 0.136149
  EX_k_e : 0.105533
  EX_mg2_e : 0.004690
  EX_ca2_e : 0.002814
  EX_cl_e : 0.002814
  EX_cu2_e : 0.000383
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991316
  EX_h2o_e : 548.202178
  EX_co2_e : 29.449555
  EX_succ_e : 0.563795
  Auxiliary production reaction : 0.285546
  EX_ura_e : 0.097861
  EX_for_e : 0.001326
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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