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 : uaccg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3614 b0910 b4152 b2925 b2097 b2781 b1850 b3617 b3844 b1612 b1611 b4122 b1759 b1200 b4374 b0675 b4138 b4123 b0621 b0153 b0590 b2406 b0452 b3918 b4042 b1517 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.554246 (mmol/gDw/h)
  Minimum Production Rate : 0.292633 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_h_e : 1000.000000
  EX_fe2_e : 999.962286
  EX_o2_e : 271.432562
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.064522
  EX_so4_e : 3.680198
  EX_pi_e : 1.119894
  EX_k_e : 0.108185
  EX_mg2_e : 0.004808
  EX_cl_e : 0.002885
  EX_ca2_e : 0.002885
  EX_cu2_e : 0.000393
  EX_mn2_e : 0.000383
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.953385
  EX_h2o_e : 548.180401
  EX_co2_e : 28.683381
  EX_h2s_e : 3.540627
  EX_succ_e : 0.577963
  Auxiliary production reaction : 0.292633
  EX_ura_e : 0.100409
  DM_mththf_c : 0.000248
  DM_5drib_c : 0.000125
  DM_4crsol_c : 0.000124

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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