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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1033 b1623 b3665 b2799 b3945 b1602 b4381 b3654 b3714 b3664 b1727 b0529 b2492 b0904 b1380 b2660 b1517 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463050 (mmol/gDw/h)
  Minimum Production Rate : 0.072048 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.206685
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.337553
  EX_pi_e : 0.518709
  EX_so4_e : 0.116605
  EX_k_e : 0.090384
  EX_fe2_e : 0.007437
  EX_mg2_e : 0.004017
  EX_cl_e : 0.002410
  EX_ca2_e : 0.002410
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.077841
  EX_co2_e : 37.237864
  EX_h_e : 4.860922
  EX_etoh_e : 1.217409
  EX_ac_e : 0.269581
  EX_hxan_e : 0.084164
  Auxiliary production reaction : 0.072048
  DM_mththf_c : 0.000207
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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