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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1241 b0351 b4069 b4384 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b2690 b1982 b3616 b3589 b2210 b0675 b0261 b0822 b1602 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.347894 (mmol/gDw/h)
  Minimum Production Rate : 1.333461 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.797640
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.758004
  EX_pi_e : 4.335965
  EX_so4_e : 0.087607
  EX_k_e : 0.067907
  EX_fe2_e : 0.005588
  EX_mg2_e : 0.003018
  EX_cl_e : 0.001811
  EX_ca2_e : 0.001811
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 50.827046
  EX_co2_e : 26.107215
  EX_h_e : 7.237383
  EX_pyr_e : 2.197508
  Auxiliary production reaction : 1.333461
  EX_ac_e : 0.508809
  DM_oxam_c : 0.000389
  DM_5drib_c : 0.000233
  EX_glyclt_e : 0.000233
  DM_4crsol_c : 0.000078

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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