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

Gene deletion strategy (85 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3399 b0474 b2518 b4069 b2502 b2744 b3708 b3008 b0910 b4152 b3115 b1849 b2296 b2926 b1612 b1611 b4122 b3962 b2797 b3117 b1814 b4471 b4267 b4374 b0675 b2361 b2291 b1701 b1805 b2799 b3945 b4138 b4123 b0621 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b0508 b0594 b3447 b4266 b1517 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439391 (mmol/gDw/h)
  Minimum Production Rate : 0.029008 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.425924
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.667552
  EX_pi_e : 0.423839
  EX_so4_e : 0.110648
  EX_k_e : 0.085766
  EX_fe2_e : 0.007057
  EX_mg2_e : 0.003812
  EX_ca2_e : 0.002287
  EX_cl_e : 0.002287
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.354743
  EX_co2_e : 35.220480
  EX_h_e : 6.131661
  EX_succ_e : 0.458194
  EX_ura_e : 0.311593
  EX_ac_e : 0.255807
  EX_trp__L_e : 0.149488
  DM_mththf_c : 0.029205
  Auxiliary production reaction : 0.029008
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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