MetNetComp Database [1] / Core Genes

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

Model : iLB1027_lipid [2].
Target metabolite : ppbng_h
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 390
  Remaining genes: PHATRDRAFT_54086 PHATRDRAFT_41812 PHATRDRAFT_52539 Phatr3_EG01455 PHATRDRAFT_44603 PHATRDRAFT_22187 PHATRDRAFT_51720 PHATRDRAFT_10356 PHATRDRAFT_32847 PHATRDRAFT_draft521 PHATRDRAFT_31465 PHATRDRAFT_18745 PHATRDRAFT_44618 PHATRDRAFT_28056 PHATRDRAFT_18398 PHATRDRAFT_14618 PHATRDRAFT_55157 Phatr3_EG01955 PHATRDRAFT_30471 PHATR_10581 PHATRDRAFT_14529 PHATRDRAFT_10068 PHATRDRAFT_30514 PHATRDRAFT_20757 PHATRDRAFT_7072 PHATRDRAFT_24739 PHATRDRAFT_51092 PHATRDRAFT_45510 PHATRDRAFT_22974 PHATRDRAFT_27726 PHATRDRAFT_50034 PHATRDRAFT_41845 PHATRDRAFT_10418 PHATRDRAFT_37652 PHATRDRAFT_23908 PHATRDRAFT_2217 PHATRDRAFT_19518 PHATRDRAFT_23247 PHATRDRAFT_18665 PHATRDRAFT_34010 PHATRDRAFT_50770 PHATRDRAFT_54082 PHATRDRAFT_54983 PHATRDRAFT_54738 PHATRDRAFT_31683 PHATRDRAFT_16722 Phatr3_EG02208 PHATRDRAFT_draft1367 PHATRDRAFT_draft417 PHATRDRAFT_13382 PHATRDRAFT_42129 PHATRDRAFT_10208 PHATRDRAFT_36139 PHATRDRAFT_16698 PHATRDRAFT_14792 Phatr3_EG02584 PHATRDRAFT_9538 PHATRDRAFT_24238 PHATRDRAFT_draft1689 PHATRDRAFT_28222 PHATRDRAFT_21201 PHATRDRAFT_20015 PHATRDRAFT_29260 PHATRDRAFT_20547 PHATRDRAFT_41856 PHATRDRAFT_25379 PHATRDRAFT_34582 PHATRDRAFT_24353 PHATRDRAFT_42447 PHATRDRAFT_13073 PHATRDRAFT_14230 Phatr3_EG02363 PHATRDRAFT_20934 PHATRDRAFT_20809 PHATRDRAFT_18228 PHATRDRAFT_42726 Phatr3_EG02241 PHATRDRAFT_15089 PHATRDRAFT_12807 PHATRDRAFT_16571 Phatr3_EG02240 PHATRDRAFT_draft913 PHATRDRAFT_41702 PHATRDRAFT_23850 PHATRDRAFT_52648 PHATRDRAFT_30572 PHATRDRAFT_54015 PHATRDRAFT_43429 Phatr3_EG02403 Phatr3_EG01923 PHATRDRAFT_21829 PHATRDRAFT_7664 PHATRDRAFT_10757 Phatr3_EG02261 PHATRDRAFT_52316 PHATRDRAFT_25204 PHATRDRAFT_18080 PHATRDRAFT_23811 PHATRDRAFT_14626 PHATRDRAFT_24772 PHATRDRAFT_20183 PHATRDRAFT_34526 PHATRDRAFT_2087 PHATRDRAFT_17401 PHATRDRAFT_44955 PHATRDRAFT_21116 PHATRDRAFT_25183 PHATRDRAFT_19692 PHATRDRAFT_26293 PHATRDRAFT_20331 PHATRDRAFT_54499 PHATRDRAFT_30113 PHATRDRAFT_26432 PHATRDRAFT_9078 PHATRDRAFT_26256 PHATRDRAFT_55057 PHATRDRAFT_42940 PHATRDRAFT_9258 PHATRDRAFT_47067 PHATRDRAFT_46657 Phatr3_EG02287 PHATRDRAFT_17772 PHATRDRAFT_8835 PHATRDRAFT_36347 PHATRDRAFT_27735 PHATRDRAFT_55086 PHATRDRAFT_31718 Phatr3_EG02309 PHATRDRAFT_9654 PHATRDRAFT_10100 PHATRDRAFT_55035 PHATRDRAFT_13265 PHATRDRAFT_33017 PHATRDRAFT_18872 PHATRDRAFT_9040 PHATRDRAFT_5629 Phatr3_EG01594 PHATRDRAFT_42282 PHATRDRAFT_3267 PHATRDRAFT_35509 Phatr3_EG02349 PHATRDRAFT_46855 PHATRDRAFT_3046 PHATRDRAFT_51811 PHATRDRAFT_41746 PHATRDRAFT_15068 PHATRDRAFT_31109 PHATRDRAFT_19324 PHATRDRAFT_18319 Phatr3_EG02614 PHATRDRAFT_18246 PHATRDRAFT_23598 PHATRDRAFT_22909 PHATRDRAFT_13951 PHATRDRAFT_4025 PHATRDRAFT_45239 Phatr3_EG02218 PHATRDRAFT_41515 PHATRDRAFT_54134 PHATRDRAFT_31906 PHATRDRAFT_30967 PHATRDRAFT_45451 PHATRDRAFT_35643 PHATRDRAFT_40163 PHATRDRAFT_19000 PHATRDRAFT_draft552 PHATRDRAFT_26346 PHATRDRAFT_45120 PHATRDRAFT_16944 PHATRDRAFT_29824 PHATRDRAFT_30690 PHATRDRAFT_13001 PHATRDRAFT_11088 PHATRDRAFT_13445 PHATRDRAFT_23547 PHATRDRAFT_18524 Phatr3_EG02219 PHATRDRAFT_11722 PHATRDRAFT_43016 PHATRDRAFT_22357 PHATRDRAFT_47250 PHATRDRAFT_43320 PHATRDRAFT_43010 PHATRDRAFT_10779 PHATRDRAFT_8982 PHATRDRAFT_28882 PHATRDRAFT_51609 PHATRDRAFT_50885 PHATRDRAFT_34392 PHATRDRAFT_28620 PHATRDRAFT_17671 PHATRDRAFT_48694 PHATRDRAFT_26970 PHATRDRAFT_26813 PHATRDRAFT_41645 PHATRDRAFT_46461 PHATRDRAFT_35594 PHATRDRAFT_11151 PHATRDRAFT_21592 PHATRDRAFT_31440 Phatr3_EG02399 PHATRDRAFT_11373 PHATRDRAFT_14260 PHATRDRAFT_16499 PHATRDRAFT_11305 PHATRDRAFT_50964 PHATRDRAFT_22919 PHATRDRAFT_42003 PHATRDRAFT_43944 PHATRDRAFT_10454 PHATRDRAFT_44902 PHATRDRAFT_10025 PHATRDRAFT_3140 PHATRDRAFT_12888 PHATRDRAFT_38891 PHATRDRAFT_37341 PHATRDRAFT_6807 PHATRDRAFT_17238 Phatr3_EG02372 PHATRDRAFT_35057 PHATRDRAFT_31662 PHATRDRAFT_3262 PHATRDRAFT_11916 PHATRDRAFT_32083 PHATRDRAFT_47395 PHATRDRAFT_46785 PHATRDRAFT_9316 PHATRDRAFT_55209 PHATRDRAFT_36821 PHATRDRAFT_54168 PHATRDRAFT_35579 PHATRDRAFT_48423 PHATRDRAFT_48664 PHATRDRAFT_39710 PHATRDRAFT_44622 PHATRDRAFT_46383 PHATRDRAFT_44584 PHATRDRAFT_31147 PHATRDRAFT_50356 PHATRDRAFT_25000 PHATRDRAFT_54756 PHATRDRAFT_29004 PHATRDRAFT_8663 PHATRDRAFT_5271 PHATRDRAFT_23639 Phatr3_EG02613 PHATRDRAFT_29658 PHATRDRAFT_12884 PHATRDRAFT_44526 PHATRDRAFT_45656 PHATRDRAFT_54709 Phatr3_EG02461 PHATRDRAFT_46193 Phatr3_EG02313 PHATRDRAFT_2171 PHATRDRAFT_27190 Phatr3_EG02286 PHATRDRAFT_39949 PHATRDRAFT_46133 PHATRDRAFT_37086 PHATRDRAFT_25769 PHATRDRAFT_12233 PHATRDRAFT_29488 Phatr3_EG01164 PHATRDRAFT_26515 PHATRDRAFT_41570 PHATRDRAFT_11016 PHATRDRAFT_49142 PHATRDRAFT_26714 PHATRDRAFT_25360 PHATRDRAFT_44831 PHATRDRAFT_28009 PHATRDRAFT_20508 PHATRDRAFT_20460 PHATRDRAFT_46830 PHATRDRAFT_34485 PHATRDRAFT_22510 PHATRDRAFT_12330 PHATRDRAFT_35819 PHATRDRAFT_44056 PHATRDRAFT_49162 PHATRDRAFT_25417 PHATRDRAFT_15125 PHATRDRAFT_11740 PHATRDRAFT_3369 Phatr3_EG00041 PHATRDRAFT_42104 PHATRDRAFT_47152 PHATRDRAFT_9348 PHATRDRAFT_17265 PHATRDRAFT_11414 PHATRDRAFT_39515 PHATRDRAFT_48112 PHATRDRAFT_1840 PHATRDRAFT_22453 PHATRDRAFT_11615 PHATRDRAFT_15797 PHATRDRAFT_18087 PHATRDRAFT_6834 PHATRDRAFT_23429 PHATRDRAFT_50149 PHATRDRAFT_51242 PHATRDRAFT_15639 PHATRDRAFT_49568 PHATRDRAFT_47999 PHATRDRAFT_47653 PHATRDRAFT_23709 PHATRDRAFT_42051 PHATRDRAFT_12171 PHATRDRAFT_15324 PHATRDRAFT_49533 Phatr3_EG02183 PHATRDRAFT_25331 PHATRDRAFT_5175 PHATRDRAFT_11281 PHATRDRAFT_8990 PHATRDRAFT_41875 PHATRDRAFT_28585 PHATRDRAFT_40433 PHATRDRAFT_44610 PHATRDRAFT_48886 PHATRDRAFT_draft18 PHATRDRAFT_15815 PHATRDRAFT_34027 PHATRDRAFT_35253 PHATRDRAFT_10970 PHATRDRAFT_31948 PHATRDRAFT_10693 Phatr_1413_bd PHATRDRAFT_45434 Phatr3_EG02454 PHATRDRAFT_42872 ADY18528_AT1 ADY18510_AT1 ADY18506_AT1 ADY18531_AT1 ADY18507_AT1 ADY18504_AT1 ADY18521_AT1 ADY18530_AT1 ADY18501_AT1 ADY18529_AT1 ADY18500_AT1 ADY18533_AT1 ADY18499_AT1 YP_874384_AT1 YP_874369_AT1 YP_874362_AT1 YP_874379_AT1 YP_874377_AT1 YP_874371_AT1 YP_874435_AT1 YP_874370_AT1 YP_874376_AT2 YP_874374_AT1 YP_874444_AT1 YP_874450_AT1 YP_874387_AT1 YP_874385_AT1 YP_874386_AT1 YP_874382_AT1 YP_874404_AT1 YP_874392_AT1 YP_874393_AT1 YP_874383_AT1 YP_874380_AT1 YP_874367_AT1 YP_874394_AT1 YP_874359_AT1 YP_874358_AT1 YP_874378_AT1 YP_874366_AT1 YP_874428_AT1 YP_874360_AT1 YP_874361_AT1 YP_874487_AT1 YP_874426_AT1 YP_874424_AT1 YP_874421_AT1 YP_874425_AT1 YP_874406_AT1 YP_874407_AT1 YP_874422_AT1 YP_874423_AT1 YP_874417_AT1 YP_874418_AT1 ADY18532_AT1 ADY18503_AT1 ADY18505_AT1 YP_874403_AT1   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.103424 (mmol/gDw/h)
  Minimum Production Rate : 0.091379 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 385.302580
  EX_co2_e : 14.848604
  EX_h2o_e : 7.854881
  EX_no3_e : 1.760000
  EX_h_e : 1.517968
  EX_so4_e : 0.054925
  EX_pi_e : 0.025681
  EX_mg2_e : 0.001848

Product: (mmol/gDw/h)
  EX_o2_e : 20.215021
  DM_indole_c : 1.071059
  SK_for_c : 0.270871
  DM_biomass_c : 0.103424
  Auxiliary production reaction : 0.091379
  DM_dmsp_c : 0.036532

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
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