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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b1241 b0351 b4384 b4152 b0871 b3617 b1612 b1611 b2883 b4122 b0477 b0261 b0411 b4138 b4123 b0621 b2406 b0114 b0529 b2492 b0904 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448105 (mmol/gDw/h)
  Minimum Production Rate : 1.457685 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.763015
  EX_o2_e : 277.030606
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.475041
  EX_pi_e : 3.347615
  EX_so4_e : 0.112842
  EX_k_e : 0.087467
  EX_mg2_e : 0.003887
  EX_ca2_e : 0.002332
  EX_cl_e : 0.002332
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992803
  EX_h2o_e : 547.191864
  EX_co2_e : 30.390735
  Auxiliary production reaction : 1.457685
  EX_succ_e : 0.467280
  EX_acald_e : 0.393989
  EX_ura_e : 0.317773
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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