MetNetComp Database [1] / Core Genes

A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iYO844 [2].
Target metabolite : pppi_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 262
  Remaining genes: BSU36850 BSU36830 BSU36800 BSU36820 BSU36860 BSU36870 BSU36880 BSU30820 BSU19310 BSU24340 BSU29200 BSU22440 BSU24350 BSU29210 BSU13910 BSU13900 BSU38630 BSU11210 BSU11200 BSU07920 BSU33040 BSU28300 BSU28310 BSU11230 BSU11240 BSU16920 BSU02270 BSU00460 BSU18000 BSU11220 BSU00500 BSU35740 BSU22830 BSU29750 BSU09300 BSU22710 BSU00760 BSU00740 BSU00750 BSU23850 BSU36590 BSU01370 BSU31350 BSU29140 BSU37150 BSU14900 BSU14190 BSU14910 BSU14920 BSU14890 BSU22540 BSU35670 BSU22560 BSU22550 BSU27250 BSU27610 BSU27260 BSU33940 BSU06440 BSU29020 BSU02230 BSU01780 BSU40420 BSU36900 BSU09540 BSU11190 BSU27270 BSU13890 BSU06520 BSU06420 BSU06430 BSU17460 BSU14610 BSU23380 BSU32170 BSU15680 BSU05740 BSU04560 BSU21870 BSU22490 BSU04640 BSU16770 BSU31400 BSU21810 BSU28080 BSU38490 BSU00780 BSU15540 BSU15530 BSU15500 BSU00770 BSU23080 BSU22700 BSU24280 BSU25160 BSU35920 BSU22750 BSU22670 BSU22680 BSU00280 BSU06490 BSU14180 BSU28390 BSU18450 BSU15570 BSU14000 BSU18440 BSU16550 BSU24270 BSU10360 BSU29440 BSU29450 BSU28680 BSU09290 BSU06360 BSU22780 BSU38280 BSU38260 BSU38270 BSU16750 BSU22740 BSU22760 BSU30540 BSU15490 BSU16760 BSU34910 BSU29620 BSU31322 BSU27870 BSU22370 BSU34920 BSU36810 BSU36840 BSU38500 BSU38530 BSU38510 BSU38520 BSU00790 BSU32260 BG12900 BSU32240 BSU21910 BSU22600 BSU02290 BSU10020 BSU34890 BSU04740 BSU29130 BSU30830 BSU34870 BSU34900 BSU22660 BSU24080 BSU27850 BSU00090 BSU29120 BSU25070 BSU00910 BSU17370 BSU00900 BSU17390 BSU28270 BSU30550 BSU28260 BSU17380 BSU28250 BSU28280 BSU15790 BSU36920 BSU28290 BSU15590 BSU36370 BSU13180 BSU15910 BSU10170 BSU08650 BSU15860 BSU15850 BSU15900 BSU24740 BSU11340 BSU25660 BSU03150 BSU11870 BSU01580 BSU24310 BSU11010 BSU30790 BSU30780 BSU16090 BSU16100 BSU11610 BSU03130 BSU33440 BSU37110 BSU35710 BSU35760 BSU22730 BSU35720 BSU36510 BSU35700 BSU25640 BSU27860 BSU35530 BSU35750 BSU35730 BSU35690 BSU35680 BSU30800 BSU11250 BSU32250 BSU24030 BSU17890 BSU24060 BSU24050 BSU17680 BSU24040 BSU15550 BSU40340 BSU15560 BSU18670 BSU33920 BSU12910 BSU15190 BSU32110 BSU22640 BSU14860 BSU22630 BSU14590 BSU14580 BSU14600 BSU15180 BSU35660 BSU30870 BSU01770 BSU23070 BSU23860 BSU36760 BSU33930 BSU15220 BSU15200 BSU16540 BSU29790 BSU15230 BSU31150 BSU04570 BSU21920 BSU12840 BSU30560 BSU22610 BSU27900 BSU16510 BSU06530 BSU22650 BSU06500 BSU34860 BSU06450 BSU06470 BSU06480 BSU06460 BSU34880 BSU00510   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.050233 (mmol/gDw/h)
  Minimum Production Rate : 0.197181 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 5.444557
  EX_glc__D_e : 1.700000
  EX_pi_e : 1.648984
  EX_nh4_e : 0.556867
  EX_k_e : 0.035480
  EX_so4_e : 0.018084
  EX_mg2_e : 0.005109
  EX_fe3_e : 0.000173
  EX_ca2_e : 0.000161

Product: (mmol/gDw/h)
  EX_h2o_e : 7.606102
  EX_co2_e : 5.036263
  EX_h_e : 1.051809
  EX_3pg_e : 0.953291
  Auxiliary production reaction : 0.197181
  EX_cmp_e : 0.027054
  EX_ac_e : 0.021455
  EX_met__L_e : 0.009529
  EX_fol_e : 0.009113

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