The eLignin Microbial Database

A curated resource for microbial metabolism of lignin-derived aromatic compounds

brinkdp/eLignin 0 0

Funneling pathway: benzoic acid

Full Name
benzoic acid
Funneling Branch
benzoyl branch
Gene Ontology
GO:0043639

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Interactive metabolic pathway map showing compounds (text labels) connected by reaction arrows. Click arrows to view reaction details, click compounds to view substrate details. Zoom with mouse wheel, pan by dragging.

Empirical Data

Organisms with this Pathway Empirical

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Organism Strain Reference(s)
Pseudomonas putida KT2440 Jiménez et al (2002)
Corynebacterium glutamicum ATCC13032 Shen et al (2012)
Acinetobacter baylyi ADP1 Collier et al (1997)
Rhodococcus opacus PD630 (DSMZ 44193) Henson et al (2018)
Amycolatopsis sp. 75iv2 (ATCC 39116) Sutherland et al (1983)
Predicted Relationships Hide predicted
The sections below contain relationships inferred from the empirical data above. They are computationally predicted and have not been independently verified. Learn more about data assumptions →
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Organisms predicted for this pathway Predicted

Inferred from reported substrate utilization: organisms that can utilise a compound entering this pathway as a reactant are predicted to carry the pathway, unless already confirmed. The reference confirming substrate use is shown. Not experimentally verified. What does this mean?

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Predicted organism Strain Inferred via substrate Reference
Acinetobacter calcoaceticus DSM 586 benzoic acid Delneri et al (1995)
Acinetobacter junii 5ga benzoic acid González et al (1993)
Acinetobacter radioresistens S13 benzoic acid Mazzoli et al (2007)
Aeromonas sp. L17 benzoic acid Deschamps et al (1980)
Aromatoleum aromaticum EbN1 benzoic acid Rabus et al (1995)
Aspergillus nidulans FGSC A4 benzoic acid Martins et al (2015)
Azoarcus anaerobius LuFRes1 benzoic acid Gorny et al (1992)
Burkholderia cepacia ATCC 29351 benzoic acid Hamzah et al (1994)
Burkholderia cepacia KK01 benzoic acid Kato et al (1998)
Burkholderia sp. VE22 benzoic acid HARAZONO et al (2003)
Comamonas testosteroni BR6020 benzoic acid Providenti et al (2001)
Cryptococcus terreus PB4 benzoic acid Bergauer et al (2005)
Cupriavidus necator JMP134 benzoic acid Pérez-Pantoja et al (2008)
Cupriavidus pinatubonensis 1245 benzoic acid Sato et al (2006)
Desulfobacterium catecholicum NZva20 benzoic acid Szewzyk et al (1987)
Desulfobacterium phenolicum Ph01 benzoic acid Bak et al (1986)
Enterobacter aerogenes L7 benzoic acid Deschamps et al (1980)
Exophiala jeanselmei CBS 658.76 benzoic acid Middelhoven (1993)
Haloferax sp. D1227 benzoic acid Emerson et al (1994)
Klebsiella pneumoniae M5a1 benzoic acid Jones et al (1990)
Leucosporidium scottii G43 benzoic acid Middelhoven (1993)
Marinobacterium georgiense KW-40 benzoic acid GONZaLEZ et al (1997)
Paraburkholderia aromaticivorans AR20-38 benzoic acid Margesin et al (2021)
Pseudomonas fluorescens AN103 benzoic acid Paulsen et al (2005)
Pseudomonas plecoglossicida G2 benzoic acid Chowdhury et al (2004)
Pseudomonas putida Perestelo isolate 3 benzoic acid Perestelo et al (1996)
Pseudomonas putida mt-2 benzoic acid Murray et al (1972)
Pseudomonas sp. Isolate 9.1 benzoic acid Ravi et al (2018)
Pseudomonas stutzeri A1501 benzoic acid Li et al (2010)
Rhodococcus erythropolis 1CP benzoic acid Eulberg et al (1997)
Rhodococcus erythropolis TA421 benzoic acid Chung et al (1994)
Rhodococcus rhodochrous 116 benzoic acid Karlson et al (1993)
Rhodopseudomonas palustris CGA001 benzoic acid Harwood et al (1988)
Rhodosporidium lusitaniae PB14 benzoic acid Bergauer et al (2005)
Rhodosporidium toruloides IFO0880 benzoic acid Yaegashi et al (2017)
Rhodotorula creatinivora PB7 benzoic acid Bergauer et al (2005)
Rhodotorula graminis WP1 benzoic acid Durham et al (1984)
Rhodotorula ingeniosa PB5 benzoic acid Bergauer et al (2005)
Sphingomonas aromaticivorans F199 benzoic acid BALKWILL et al (1997)
Sulfuritalea hydrogenivorans sk43H benzoic acid Sperfeld et al (2018)
Thauera aromatica K172 benzoic acid Tschech et al (1987)
Thauera sp. Cin3,4 benzoic acid Mechichi et al (2005)
Trichosporon cutaneum CBS2466 benzoic acid Middelhoven (1993)

Predicted enzyme assignments for confirmed organisms Predicted

Inferred from confirmed pathway membership: if an organism is confirmed to carry this pathway, enzymes known to catalyse reactions within it are predicted to be present. The reference confirming the organism’s membership of this pathway is shown. Not experimentally verified. What does this mean?

Organism Strain Predicted enzyme Reference confirming pathway
Corynebacterium glutamicum ATCC13032 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase Shen et al (2012)
Acinetobacter baylyi ADP1 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase Collier et al (1997)
Rhodococcus opacus PD630 (DSMZ 44193) 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase Henson et al (2018)
Amycolatopsis sp. 75iv2 (ATCC 39116) 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase Sutherland et al (1983)
Corynebacterium glutamicum ATCC13032 Benzoate 1,2-dioxygenase Shen et al (2012)
Acinetobacter baylyi ADP1 Benzoate 1,2-dioxygenase Collier et al (1997)
Rhodococcus opacus PD630 (DSMZ 44193) Benzoate 1,2-dioxygenase Henson et al (2018)
Amycolatopsis sp. 75iv2 (ATCC 39116) Benzoate 1,2-dioxygenase Sutherland et al (1983)

Reactions in this Pathway

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Order Substrates Products Enzyme(s) Reaction
1 benzoic acid → 3,5-cyclohexadiene-1,2-diol-1-carboxylate Benzoate 1,2-dioxygenase R00014
2 3,5-cyclohexadiene-1,2-diol-1-carboxylate → catechol 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase R00015

Compounds (Substrates & Products)

Intermediate metabolites that are not registered in the Substrate table are shown as plain text without a hyperlink.

Compound Name Formula SMILES PubChem Role
benzoic acid C7H6O2 C1=CC=C(C=C1)C(=O)O 243 substrate
3,5-cyclohexadiene-1,2-diol-1-carboxylate (intermediate) C7H7O4- C1=CC(C(C=C1)(C(=O)[O-])O)O 9543121 product, substrate
catechol C6H6O2 C1=CC=C(C(=C1)O)O 289 product

Connected Pathways

Outgoing Connections (This pathway connects to:)

Connected Pathway Connecting Compound
Fission pathway: beta-ketoadipate: Catechol branch catechol
Fission pathway: beta-ketoadipate (all branches) catechol
Fission pathway: catechol meta-cleavage catechol

Genes

Gene Enzyme
Pp_benA Benzoate 1,2-dioxygenase
Pp_benB Benzoate 1,2-dioxygenase
Pp_benD 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase

Other Databases

Database Comment
MetaCyc Metabolic pathway database

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