The eLignin Microbial Database

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

brinkdp/eLignin 0 0

Sphingobium sp. SYK-6

Kingdom
Bacteria
Phylum
Proteobacteria
Class
Alpha-proteobacteria
Type
Gram negative
Strain
SYK-6
Origin (Details)
Pulp-bleaching wastewater, Japan
Origin (Category)
Pulp and Paper Mill effluent
Genome Sequenced
Yes
Synonyms
Pseudomonas paucimobilis
Chromobacterium devorans
Sphingomonas paucimobilis
Empirical Data

Utilizible (lignin-derived) carbon sources (13) Empirical

NB! Always check the primary references for the experimental details; "utilizable" does not necessarily equal "growth-supporting".

📥 Download as TSV
Substrate Reference(s) Comment(s)
4-hydroxybenzoic acid Katayama et al (1988) -
5-carboxyvanillic acid Katayama et al (1988) -
biphenyl Masai et al (1991) -
ddva (5,5-dehydrodivanillate) Katayama et al (1988) -
dehydropolymerisate (dhp) Masai et al (1991)
MASAI et al (2007) 		-
ferulic acid Masai et al (2002) -
gallic acid Kasai et al (2005) -
guaiacylglycerol-beta-guaiacyl ether Masai et al (1989) -
pinoresinol Masai et al (1991)
MASAI et al (2007) 		-
syringaldehyde MASAI et al (2007) -
syringic acid Katayama et al (1988)
Masai et al (2004) 		-
vanillic acid Katayama et al (1988) -
vanillin MASAI et al (2007) -

Pathways (7) Empirical

📥 Download as TSV
Pathway Name Reference(s)
ferulic acid Masai et al (2002)
protocatechuate 4,5-cleavage Peng et al (2005)
sinapic acid -
syringic acid I MASAI et al (2007)
syringic acid II MASAI et al (2007)
syringic acid III MASAI et al (2007)
vanillin I Abe et al (2005)

Enzymes (14) Empirical

📥 Download as TSV
Enzyme Gene(s) Reference(s)
2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase - -
2-pyrone-4,6-dicarboxylate hydrolase - -
2-pyrone-4,6-dicarboxylate lactonase - -
3-O-methylgallate 3,4-dioxygenase - -
4-oxalomesaconate hydratase - -
Feruloyl-CoA synthase - -
gallate dioxygenase - -
oxaloacetate decarboxylase - -
pinoresinol reductase Sph_pinZ Fukuhara et al (2013)
protocatechuate 4,5-dioxygenase - -
syringate O-demethylase - -
trans-feruloyl-CoA hydratase - -
Vanillate monooxygenase - -
Vanillin dehydrogenase - -

Transporters (0) Empirical

No transporters listed for this organism.

Genes (15) Empirical

📥 Download as TSV
Gene Name Reference(s)
Sph_desA Masai et al (2004)
Sph_desB Kasai et al (2005)
Sph_desZ Kasai et al (2004)
Sph_ferA Masai et al (2002)
Sph_ferB Masai et al (2002)
Sph_ferB2 Masai et al (2002)
Sph_ligA Noda et al (1990)
Sph_ligB Noda et al (1990)
Sph_ligC Masai et al (2000)
Sph_ligI Masai et al (1999)
Sph_ligJ Hara et al (2000)
Sph_ligK Hara et al (2003)
Sph_ligM Abe et al (2005)
Sph_ligV MASAI et al (2007)
Sph_pinZ Fukuhara et al (2013)
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 →
Predicted sections are hidden. Show them

Predicted pathways in Sphingobium sp. SYK-6 Predicted

Inferred from reported utilizable carbon sources: if the organism can utilise a compound that enters a pathway as a reactant, it may carry that pathway. Not experimentally verified. What does this mean?

📥 Download as TSV
Predicted pathway Funneling branch Inferred via substrate Reference
guaiacol coniferyl branch vanillic acid Katayama et al (1988)
p-coumaric acid p-coumaric branch 4-hydroxybenzoic acid Katayama et al (1988)
vanillin II coniferyl branch vanillic acid, vanillin Katayama et al (1988), MASAI et al (2007)

Predicted enzymes in Sphingobium sp. SYK-6 Predicted

Inferred from confirmed pathways: if the organism is confirmed to carry a pathway, enzymes known to catalyse reactions in that pathway are predicted to be present. The pathway used for each inference is shown. Not experimentally verified. What does this mean?

Predicted enzyme Inferred via pathway Reference
4-oxalmesaconate hydratase syringic acid III MASAI et al (2007)
4-oxalomesaconate tautomerase syringic acid II MASAI et al (2007)
HMG aldolase syringic acid III MASAI et al (2007)

Culture Collections

Strain Depository ID
SYK-6 NBRC 103272

Genome Sequencing

Strain Status Reference
SYK-6 Yes Masai et al (2012)

Other Databases

Database Comment
NCBI Taxonomy Taxonomy database
PATRIC Genome sequence database

← Back to Organisms List