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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (113 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b2744 b3614 b0910 b4152 b2297 b2458 b2781 b3617 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b1033 b4374 b0675 b1602 b4138 b4123 b0621 b2913 b4381 b0529 b1380 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504660 (mmol/gDw/h)
  Minimum Production Rate : 0.266534 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.682476
  EX_o2_e : 279.435824
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.983351
  EX_pi_e : 1.019865
  EX_so4_e : 0.127083
  EX_k_e : 0.098506
  EX_mg2_e : 0.004378
  EX_ca2_e : 0.002627
  EX_cl_e : 0.002627
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991895
  EX_h2o_e : 546.099553
  EX_co2_e : 29.851877
  EX_ac_e : 1.528548
  EX_succ_e : 0.526255
  Auxiliary production reaction : 0.266534
  EX_3hpp_e : 0.091345
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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