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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3617 b2407 b1004 b3713 b1109 b0046 b1982 b2210 b1033 b3665 b1602 b4381 b2406 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b3662 b1813 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379141 (mmol/gDw/h)
  Minimum Production Rate : 1.453736 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.047122
  EX_o2_e : 284.521660
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.003442
  EX_pi_e : 1.819458
  EX_so4_e : 0.095475
  EX_k_e : 0.074006
  EX_mg2_e : 0.003289
  EX_cl_e : 0.001973
  EX_ca2_e : 0.001973
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993911
  EX_h2o_e : 551.885032
  EX_co2_e : 34.604772
  Auxiliary production reaction : 1.453736
  EX_ac_e : 0.554339
  EX_ade_e : 0.000255
  EX_mththf_e : 0.000170
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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