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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b1479 b2297 b2458 b3617 b0030 b2407 b3236 b2463 b1982 b2210 b3551 b0261 b4219 b1832 b1778 b2406 b0114 b0529 b2492 b0904 b1710 b2480 b3662 b0606 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504600 (mmol/gDw/h)
  Minimum Production Rate : 1.934554 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.677422
  EX_nh4_e : 11.254654
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.486740
  EX_so4_e : 0.127068
  EX_k_e : 0.098494
  EX_mg2_e : 0.004377
  EX_fe2_e : 0.004164
  EX_fe3_e : 0.003940
  EX_ca2_e : 0.002626
  EX_cl_e : 0.002626
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.687707
  EX_co2_e : 18.292789
  EX_h_e : 12.236938
  Auxiliary production reaction : 1.934554
  EX_ac_e : 0.737771
  EX_mal__L_e : 0.526872
  EX_xan_e : 0.000340
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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