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 : uacmamu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b4382 b1241 b0351 b4069 b4384 b2744 b1278 b3614 b0910 b4152 b2297 b2458 b2925 b2097 b2781 b1850 b3617 b1612 b1611 b4122 b1759 b1200 b4374 b0675 b4138 b4123 b0621 b2406 b3918 b0494 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.552571 (mmol/gDw/h)
  Minimum Production Rate : 0.291837 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.656044
  EX_o2_e : 267.472926
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.043264
  EX_pi_e : 1.116688
  EX_so4_e : 0.139148
  EX_k_e : 0.107858
  EX_mg2_e : 0.004794
  EX_cl_e : 0.002876
  EX_ca2_e : 0.002876
  EX_cu2_e : 0.000392
  EX_mn2_e : 0.000382
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991125
  EX_h2o_e : 536.652394
  EX_co2_e : 17.486614
  EX_dha_e : 3.840696
  EX_succ_e : 0.576216
  EX_ac_e : 0.321699
  Auxiliary production reaction : 0.291837
  EX_ura_e : 0.100017
  DM_mththf_c : 0.000248
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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