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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b1478 b3399 b3942 b1732 b1241 b0351 b4069 b2744 b2297 b2458 b0160 b1004 b3713 b1109 b0046 b3124 b2463 b1982 b3616 b3589 b2210 b0675 b2361 b3551 b0261 b1602 b4219 b1832 b1778 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b0514 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.315501 (mmol/gDw/h)
  Minimum Production Rate : 0.596394 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.192170
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.616934
  EX_pi_e : 1.497123
  EX_so4_e : 0.079450
  EX_k_e : 0.061584
  EX_mg2_e : 0.002737
  EX_fe2_e : 0.002604
  EX_fe3_e : 0.002463
  EX_ca2_e : 0.001642
  EX_cl_e : 0.001642
  EX_cu2_e : 0.000224
  EX_mn2_e : 0.000218
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 52.685509
  EX_co2_e : 32.349507
  EX_h_e : 6.984467
  EX_ac_e : 1.066293
  Auxiliary production reaction : 0.596394
  EX_xan_e : 0.008255
  EX_ade_e : 0.000353
  DM_5drib_c : 0.000212
  DM_4crsol_c : 0.000070

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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