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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b2836 b1478 b1241 b3831 b4069 b3614 b0910 b4152 b2297 b2458 b2781 b0030 b1851 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0651 b2162 b1759 b0411 b1602 b4388 b4138 b4123 b0621 b4381 b0529 b1380 b3918 b4042 b2660 b1206 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484046 (mmol/gDw/h)
  Minimum Production Rate : 0.255647 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.165678
  EX_o2_e : 283.052877
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.738952
  EX_pi_e : 0.978207
  EX_so4_e : 0.121893
  EX_k_e : 0.094482
  EX_mg2_e : 0.004199
  EX_ca2_e : 0.002519
  EX_cl_e : 0.002519
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992226
  EX_h2o_e : 549.035951
  EX_co2_e : 33.451936
  EX_succ_e : 0.504760
  EX_ac_e : 0.281805
  Auxiliary production reaction : 0.255647
  EX_3hpp_e : 0.087614
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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