MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : pheme_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 19
  Gene deletion: STM1469 STM0761 STM1468 STM4300 STM2285 STM4568 STM1570 STM1620 STM4036 STM2081 STM1211 STM2317 STM3179 STM4301 STM3599 STM4325 STM0627 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.204918 (mmol/gDw/h)
  Minimum Production Rate : 0.030707 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 6.966863
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.521835
  EX_pi_e : 0.181726
  EX_k_e : 0.036394
  EX_fe2_e : 0.032209
  EX_so4_e : 0.024996
  EX_mg2_e : 0.001618
  EX_ca2_e : 0.000971
  EX_cl_e : 0.000971
  EX_cobalt2_e : 0.000647
  EX_cu2_e : 0.000647
  EX_mn2_e : 0.000647
  EX_mobd_e : 0.000647
  EX_zn2_e : 0.000647

Product: (mmol/gDw/h)
  EX_h2o_e : 14.069690
  EX_h_e : 8.954279
  EX_co2_e : 6.839911
  EX_ac_e : 6.162973
  EX_for_e : 0.175879
  EX_succ_e : 0.170374
  EX_4abz_e : 0.140779
  EX_pheme_e : 0.030707
  EX_glyclt_e : 0.010246
  DM_hmfurn_c : 0.000091

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
Contact