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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b2836 b3553 b4382 b1241 b0351 b4069 b4384 b3708 b1479 b2297 b2458 b2926 b0030 b2407 b3236 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b3665 b1415 b1014 b3945 b3709 b1907 b2406 b3161 b0112 b3654 b3714 b3664 b4265 b0114 b1539 b2492 b0904 b1533 b3927 b1380 b0325 b1473 b0494 b0594 b1511 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.276980 (mmol/gDw/h)
  Minimum Production Rate : 0.294831 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.803866
  EX_o2_e : 282.505023
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.295085
  EX_pi_e : 1.151669
  EX_so4_e : 0.604491
  EX_k_e : 0.054065
  EX_mg2_e : 0.002403
  EX_ca2_e : 0.001442
  EX_cl_e : 0.001442
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000191
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000089

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995551
  EX_h2o_e : 549.744031
  EX_co2_e : 33.991730
  EX_ac_e : 2.001918
  Auxiliary production reaction : 0.294831
  EX_met__L_e : 0.239911
  EX_dxylnt_e : 0.000185
  EX_mththf_e : 0.000124
  DM_5drib_c : 0.000062
  DM_4crsol_c : 0.000062

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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