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 : udpglcur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b1478 b1241 b3831 b1278 b3614 b0910 b3926 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b3945 b4138 b4123 b0621 b2913 b4381 b2239 b2406 b2943 b3453 b2197 b3825 b3918 b2240 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.684438 (mmol/gDw/h)
  Minimum Production Rate : 0.361483 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.663407
  EX_o2_e : 273.117304
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.362612
  EX_pi_e : 1.383179
  EX_so4_e : 0.172355
  EX_k_e : 0.133598
  EX_mg2_e : 0.005938
  EX_ca2_e : 0.003563
  EX_cl_e : 0.003563
  EX_cu2_e : 0.000485
  EX_mn2_e : 0.000473
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989007
  EX_h2o_e : 546.150869
  EX_co2_e : 23.134260
  EX_succ_e : 0.713727
  Auxiliary production reaction : 0.361483
  EX_ura_e : 0.123885
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000153

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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