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Microbe : Sphingobium sp.

Microbe Description

NBRC No. 103272
Scientific name Sphingobium sp.
Synonymous name Not assigned
History Nagaoka Univ. Technol. (E. Masai, SYK-6) <- Tokyo Univ. Agriculture Technol. (Y. Katayama) <- Univ. Tokyo (M. Yamasaki)
Other culture collection No.
Other No. SYK-6
Reference
2185230
Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis. (J Bacteriol. 1990)
2737293
Detection and localization of a new enzyme catalyzing the beta-aryl ether cleavage in the soil bacterium (Pseudomonas paucimobilis SYK-6). (FEBS Lett. 1989)
8495726
A bacterial enzyme degrading the model lignin compound beta-etherase is a member of the glutathione-S-transferase superfamily. (FEBS Lett. 1993)
9647824
Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme. (Appl Environ Microbiol. 1998)
12200295
Cloning and characterization of the ferulic acid catabolic genes of Sphingomonas paucimobilis SYK-6. (Appl Environ Microbiol. 2002)
12486039
Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6. (J Bacteriol. 2003)
12618439
Roles of the enantioselective glutathione S-transferases in cleavage of beta-aryl ether. (J Bacteriol. 2003)
15090517
A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate. (J Bacteriol. 2004)
15262932
Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6. (J Bacteriol. 2004)
15743951
A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. (J Bacteriol. 2005)
16030198
Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6. (J Bacteriol. 2005)
16151081
A second 5-carboxyvanillate decarboxylase gene, ligW2, is important for lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6. (Appl Environ Microbiol. 2005)
17213657
Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. (Biosci Biotechnol Biochem. 2007)
17645527
Degradation of 3-O-methylgallate in Sphingomonas paucimobilis SYK-6 by pathways involving protocatechuate 4,5-dioxygenase. (FEMS Microbiol Lett. 2007)

Functional Potential >>Details

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TypePattern Component Gene CDS
Alanine racemization(NFUNC_0063)
RequireA
ALR
(NRULE_0228)
Alanine racemaseSLG_24650
Ampicillin resistance(NFUNC_0046)
RequireA
BLAA
(NRULE_0122)
Beta-lactamase class ASLG_01940
Anthranilate biosynthesis(NFUNC_0038)
RequireA
GLAT
(NRULE_0142)
Glutamine amidotransferaseSLG_25880
TRPE
(NRULE_0143)
Anthranilate synthase component ISLG_25840
Aromatic azo compounds degradation(NFUNC_0073)
RequireA
AZOR
(NRULE_0236)
FMN-dependent NADH-azoreductaseSLG_06410
Arsenical resistance(NFUNC_0004)
RequireD
ARSB2
(NRULE_0016)
Arsenite resistance protein ArsBSLG_06260 SLG_p_01420
ARSC1
(NRULE_0017)
Arsenate reductaseSLG_p_01430 SLG_16250 SLG_06250
E
ARSB2
(NRULE_0016)
Arsenite resistance protein ArsBSLG_06260 SLG_p_01420
ARSC2
(NRULE_0018)
Arsenate reductaseSLG_p_01440
Participant 
ARSH
(NRULE_0021)
ArsH proteinSLG_p_01400
Bacitracin resistance(NFUNC_0022)
RequireA
UPPP
(NRULE_0097)
Undecaprenyl-diphosphataseSLG_29270
Beta-lactam antibiotic resistance(NFUNC_0033)
RequireA
BLAA
(NRULE_0122)
Beta-lactamase class ASLG_01940
Bioplastic degradation(NFUNC_0015)
RequireA
PHAZ1
(NRULE_0023)
Intracellular poly(3-hydroxyalkanoate) depolymeraseSLG_14530
Bioplastic synthesis(NFUNC_0001)
RequireA
PHAC1
(NRULE_0010)
Poly(3-hydroxyalkanoate) polymeraseSLG_06210
Participant 
PHAB
(NRULE_0011)
Acetoacetyl-CoA reductaseSLG_38730
 
PHAP1
(NRULE_0374)
PhasinSLG_06220
Ectoine biosynthesis(NFUNC_0056)
RequireA
ECTB
(NRULE_0186)
Diaminobutyrate--2-oxoglutarate transaminaseSLG_08050
ECTA
(NRULE_0187)
L-2,4-diaminobutyric acid acetyltransferaseSLG_08040
ECTC
(NRULE_0188)
L-ectoine synthaseSLG_08060
Hydroxyectoine biosynthesis(NFUNC_0057)
RequireA
ECTD
(NRULE_0189)
Ectoine hydroxylaseSLG_08070
Participant 
ECTB
(NRULE_0186)
Diaminobutyrate--2-oxoglutarate transaminaseSLG_08050
 
ECTA
(NRULE_0187)
L-2,4-diaminobutyric acid acetyltransferaseSLG_08040
 
ECTC
(NRULE_0188)
L-ectoine synthaseSLG_08060
Mercury resistance(NFUNC_0005)
RequireA
MERA
(NRULE_0008)
Mercuric reductaseSLG_p_00120
Metal-binding protein(NFUNC_0105)
RequireC
MODA
(NRULE_0324)
Molybdate ABC transporter substrate-binding proteinSLG_32540 SLG_35210
E
CUER
(NRULE_0328)
Copper-responsive transcriptional regulator CueRSLG_p_00890
F
SOXR
(NRULE_0329)
Redox-sensitive transcriptional activator SoxRSLG_23740
Molybdate transport (ABC transporter)(NFUNC_0097)
RequireA
MODA
(NRULE_0324)
Molybdate ABC transporter substrate-binding proteinSLG_32540 SLG_35210
Participant 
MODB
(NRULE_0325)
Molybdate ABC transporter permease proteinSLG_32530
 
MODC
(NRULE_0326)
Molybdate ABC transporter ATP-binding proteinSLG_32520
Penicillin resistance(NFUNC_0047)
RequireA
BLAA
(NRULE_0122)
Beta-lactamase class ASLG_01940
Phenol degradation(NFUNC_0028)
RequireB
PHEA1
(NRULE_0083)
Aromatic ring hydroxylaseSLG_11330
Participant 
FDR1
(NRULE_0032)
Oxygenase electron transfer componentSLG_p_00600
 
FDX1
(NRULE_0034)
Putative Rieske-type ferredoxinSLG_16640 SLG_34970 SLG_34870 SLG_34280 SLG_32620 SLG_27710 SLG_19120 SLG_18880 SLG_18730 SLG_18530 SLG_18370 SLG_07770 SLG_07580 SLG_05220
 
FADR1
(NRULE_0101)
NADH-dependent flavin reductaseSLG_19070 SLG_34820 SLG_03810 SLG_11320
Phytic acid hydrolysis(NFUNC_0085)
RequireA
PHYT
(NRULE_0258)
3-phytaseSLG_11510
Trehalose biosynthesis (from maltooligosaccharide)(NFUNC_0037)
RequireA
TREY
(NRULE_0140)
Maltooligosyl trehalose synthaseSLG_10390
TREZ
(NRULE_0141)
Malto-oligosyltrehalose trehalohydrolaseSLG_10400
Participant 
GLGX
(NRULE_0139)
Glycogen debranching enzymeSLG_08630 SLG_10410

Genomic Overview

BioProject IDPRJNA67115
Locus_tagSLG
INSDC entriesAP012222
Sequence statusComplete
Current status
Contig number2
Size(bp) 4,348,133
Gene 4,063
Finishing goal
Assembly methodphred/phrap v. 0.020425.c
Coverage8.0x
Technology
  • Sanger ABI3730
Reference
  • Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls. (J Bacteriol. 2012) PMID: 22207743

Data Download

Genomic nucleotide sequence Nucleotide sequence of the coding regions Translation of the coding sequneces List of genes / ORFs
FASTA
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FASTA
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FASTA
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TSV
uncompressed
1.3 MB 1.2 MB 803.9 KB 305.9 KB