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 : damp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1478 b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b2925 b2097 b3617 b2407 b2690 b0675 b0822 b0114 b0529 b2492 b0904 b0515 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.464279 (mmol/gDw/h)
  Minimum Production Rate : 0.502294 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.623852
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.532893
  EX_pi_e : 0.950140
  EX_so4_e : 0.116915
  EX_k_e : 0.090624
  EX_fe2_e : 0.007457
  EX_mg2_e : 0.004028
  EX_cl_e : 0.002417
  EX_ca2_e : 0.002417
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.566674
  EX_co2_e : 26.855394
  EX_h_e : 9.195442
  EX_pyr_e : 2.410743
  EX_acald_e : 0.912316
  Auxiliary production reaction : 0.502294
  EX_alltn_e : 0.001813
  DM_mththf_c : 0.000208
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000104

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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