The eLignin Microbial Database

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

brinkdp/eLignin 0 0

Funneling pathway: vanillin II

Full Name
vanillin II
Funneling Branch
coniferyl branch

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Empirical Data

Organisms with this Pathway Empirical

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Organism Strain Reference(s)
Rhodococcus opacus PD630 (DSMZ 44193) Henson et al (2018)
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
Acetobacterium dehalogenans MC vanillic acid Kaufmann et al (1998)
Acetobacterium woodii NZva16 vanillic acid, vanillin Bache et al (1981)
Acinetobacter baumannii KMB1 vanillin Kuhnigk et al (1997)
Acinetobacter baylyi ADP1 vanillic acid Salvachúa et al (2015), Fischer et al (2008)
Acinetobacter calcoaceticus DSM 586 vanillic acid Delneri et al (1995)
Alcaligenes faecalis KD10 vanillin Kuhnigk et al (1997)
Amycolatopsis sp. 75iv2 (ATCC 39116) vanillic acid, vanillin Pometto III et al (1981), Sutherland et al (1983), Davis et al (2012)
Azotobacter vinelandii NBRC13581 vanillic acid, vanillin Hirose et al (2013)
Bacillus cereus KD4 vanillin Kuhnigk et al (1997)
Bacillus licheniformis KB1 vanillin Kuhnigk et al (1997)
Bacillus subtilis KD8 vanillin Kuhnigk et al (1997)
Bradyrhizobium japonicum USDA110 vanillic acid Sudtachat et al (2009)
Brettanomyces anomalus NCYC 615 vanillin Edlin et al (1995)
Burkholderia cepacia KF12 vanillin Kuhnigk et al (1997)
Burkholderia cepacia KK01 vanillic acid Kato et al (1998)
Burkholderia cepacia Song isolate 1 vanillic acid -
Burkholderia sp. VE22 vanillin HARAZONO et al (2003)
Citrobacter sp. VA53 vanillin HARAZONO et al (2003)
Clostridium methoxybenzovorans SR3 vanillic acid, vanillin Mechichi et al (2005)
Clostridium thermoaceticum ATCC 39073 vanillic acid Daniel et al (1988)
Comamonas acidovorans KNB3 vanillin Kuhnigk et al (1997)
Comamonas sp. B-9 (CGMCC No. 4251) vanillic acid Chen et al (2012)
Comamonas testosteroni BR6020 vanillic acid Providenti et al (2006)
Comamonas testosteroni CNB-1 vanillic acid Ni et al (2012)
Cupriavidus laharis 1263a vanillic acid Sato et al (2006)
Exophiala jeanselmei CBS 658.76 vanillic acid Middelhoven (1993)
Flavobacterium lutescens NBRC3084 vanillic acid, vanillin Hirose et al (2013)
Fusarium oxysporum 4287 vanillic acid Michielse et al (2012)
Klebsiella sp. LLC-3 vanillic acid, vanillin Hirose et al (2013)
Leucosporidium scottii G43 vanillic acid Middelhoven (1993)
Marinobacterium georgiense KW-40 vanillic acid GONZaLEZ et al (1997)
Mesorhizobium sp. PT04 vanillic acid Tian et al (2016)
Microbacterium phyllosphaerae A1.1 vanillic acid Taylor et al (2012)
Microbulbifer hydrolyticus IRE-31 vanillic acid GONZaLEZ et al (1997)
Micrococcus luteus E1.1 vanillic acid Taylor et al (2012)
Nocardia sp. KD19 vanillin Kuhnigk et al (1997)
Oceanimonas doudoroffii JCM21046T vanillic acid Numata et al (2015)
Ochrobactrum pseudogrignonense A4.3 vanillic acid Taylor et al (2012)
Ochrobactrum rhizosphaerae C4.1 vanillic acid Taylor et al (2012)
Ochrobactrum sp. LLC-2 vanillic acid, vanillin Hirose et al (2013)
Paenibacillus glucanolyticus SLM1 vanillin Mathews et al (2014)
Pandoraea norimbergensis LD001 vanillic acid, vanillin Bandounas et al (2011)
Pantoea dispersa Song isolate 2 vanillic acid Song (2009)
Penicillium chrysogenum MUCL 31363 vanillin Rodríguez et al (1994)
Phanerochaete chrysosporium ATCC 34541 vanillin Nakamura et al (2011)
Pseudomonas aeruginosa KMD3 vanillin Kuhnigk et al (1997)
Pseudomonas chlororaphis subsp. aureofaciens PT02 vanillic acid, vanillin Tian et al (2016)
Pseudomonas citronellolis KMA4 vanillin Kuhnigk et al (1997)
Pseudomonas fluorescens AN103 vanillic acid, vanillin Paulsen et al (2005), Narbad et al (1998)
Pseudomonas fluorescens DSM 50090 vanillic acid, vanillin Ravi et al (2018)
Pseudomonas mira V2 vanillic acid Jurková et al (1993)
Pseudomonas putida F1 vanillic acid, vanillin Hirose et al (2013)
Pseudomonas putida KT2440 vanillic acid, vanillin Salvachúa et al (2015), Ravi et al (2017)
Pseudomonas putida Perestelo isolate 3 vanillic acid, vanillin Perestelo et al (1996)
Pseudomonas sp. HR199 vanillic acid, vanillin Overhage et al (1999)
Pseudomonas sp. Isolate 9.1 vanillic acid, vanillin Ravi et al (2018)
Pseudomonas sp. KF704 vanillic acid, vanillin Hirose et al (2013)
Pseudomonas sp. LLC-1 vanillic acid, vanillin Hirose et al (2013), Hirose et al (2020)
Rhizobium sp. YS-1r vanillic acid Jackson et al (2017)
Rhodococcus erythropolis A5.1 vanillic acid Taylor et al (2012)
Rhodococcus fascians AY730713 vanillic acid Song (2009)
Rhodococcus fascians Song isolate 3 vanillic acid Song (2009)
Rhodococcus jostii RHA1 vanillic acid, vanillin Salvachúa et al (2015), Chen et al (2012)
Rhodococcus opacus DSM 1069 vanillic acid Kosa et al (2011)
Rhodococcus sp. UKMP-5M vanillic acid, vanillin Azman (2015)
Rhodopseudomonas palustris CGA001 vanillic acid Harwood et al (1988)
Rhodosporidiobolus colostri DBVPG 10655 vanillic acid Margesin et al (2022)
Rhodosporidium toruloides IFO0880 vanillic acid Yaegashi et al (2017)
Rhodotorula sp. R2 vanillic acid Hainal et al (2012)
Rhodotorula mucilaginosa CBS17 vanillic acid Sampaio (1999)
Rhodotorula rubra IFO 889 vanillic acid Huang et al (1993)
Serratia liquefaciens sp. PT01 vanillic acid, vanillin Tian et al (2016)
Serratia marcescens C5 vanillic acid Rhoads et al (1995)
Serratia marcescens Perestelo isolate 2 vanillin Perestelo et al (1989)
Serratia sp. JHT01 vanillic acid, vanillin Tian et al (2016)
Sphingobacterium sp. T2 vanillic acid Taylor et al (2012)
Sphingobium sp. SYK-6 vanillic acid, vanillin Katayama et al (1988), MASAI et al (2007)
Stenotrophomonas sp. PT03 vanillic acid Tian et al (2016)
Streptomyces sp. D7 vanillic acid Chow et al (1999)
Streptomyces viridosporus T7A vanillin Pometto et al (1983)

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
Rhodococcus opacus PD630 (DSMZ 44193) Vanillate monooxygenase Henson et al (2018)
Rhodococcus opacus PD630 (DSMZ 44193) Vanillin dehydrogenase Henson et al (2018)

Reactions in this Pathway

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Order Substrates Products Enzyme(s) Reaction
1 vanillin → vanillic acid Vanillin dehydrogenase R00024
2 vanillic acid → protocatechuic acid + formaldehyde Vanillate monooxygenase R00023

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
vanillin C8H8O3 COC1=C(C=CC(=C1)C=O)O 1183 substrate
vanillic acid C8H8O4 COC1=C(C=CC(=C1)C(=O)O)O 8468 product, substrate
protocatechuic acid C7H6O4 C1=CC(=C(C=C1C(=O)O)O)O 72 product
formaldehyde (intermediate) CH2O C=O 712 product

Connected Pathways

Outgoing Connections (This pathway connects to:)

Connected Pathway Connecting Compound
Fission pathway: beta-ketoadipate: Protocatechuate branch protocatechuic acid
Fission pathway: beta-ketoadipate (all branches) protocatechuic acid

Incoming Connections (Pathways connecting to this one:)

Source Pathway Connecting Compound
Funneling pathway: ferulic acid vanillin
Fission pathway: protocatechuate 4,5-cleavage protocatechuic acid
Fission pathway: protocatechuate 2,3-cleavage protocatechuic acid

Genes

Gene Enzyme
Sph_ligV Vanillin dehydrogenase
Pp_vdh Vanillin dehydrogenase
Sph_ligM Vanillate monooxygenase

Other Databases

Database Comment
MetaCyc Metabolic pathway database

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