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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b2779 b0030 b2407 b1612 b1611 b4122 b3616 b3589 b4381 b0114 b0529 b2492 b0904 b0515 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.536581 (mmol/gDw/h)
  Minimum Production Rate : 0.580516 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.505739
  EX_o2_e : 271.758599
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.803404
  EX_pi_e : 1.678620
  EX_so4_e : 0.135122
  EX_k_e : 0.104737
  EX_mg2_e : 0.004655
  EX_ca2_e : 0.002793
  EX_cl_e : 0.002793
  EX_cu2_e : 0.000380
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991382
  EX_h2o_e : 543.685332
  EX_co2_e : 26.055842
  Auxiliary production reaction : 0.580516
  EX_fum_e : 0.563732
  EX_acald_e : 0.473874
  EX_alltn_e : 0.002095
  DM_mththf_c : 0.000240
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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