SUPERFAMILY 1.75 HMM library and genome assignments server

FMN-linked oxidoreductases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   FMN-linked oxidoreductases [ 51395]
Families:   FMN-linked oxidoreductases [ 51396] (18)


Superfamily statistics
Genomes (3,170) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 28,338 145,394 53
Proteins 28,142 145,265 53


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism metabolic process0.54030.0003221Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process11Least InformativeInherited
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.0016450.002989Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.24350.06782Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.029530.0004237Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.1140.01537Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.21340.00041Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)multi-organism process0.17531Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.049460.04653Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.93331Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.27170.9403Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.21030.5705Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.54161Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process10.8613Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.0064350.07407Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0045530.4293Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.30910.6169Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0044630.00003843Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.05840.2744Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.015240.00000000003292Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.073230.07089Moderately InformativeInherited
Biological Process (BP)gene expression0.074130.8036Moderately InformativeInherited
Biological Process (BP)RNA modification0.00000018980.00000005961InformativeDirect
Biological Process (BP)ncRNA metabolic process0.000024350.0001392InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.000000011630InformativeDirect
Biological Process (BP)phospholipid metabolic process0.0080790.06087InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.011610.1821InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0051320.00006294InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.29430.4479InformativeInherited
Biological Process (BP)RNA processing0.00011960.0111InformativeInherited
Biological Process (BP)lactate metabolic process0.00076550.00004544Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.00000000037350Highly InformativeDirect
Biological Process (BP)photorespiration0.000000028550.0000000006945Highly InformativeDirect
Biological Process (BP)modification of morphology or physiology of other organism0.0000048320.00006311Highly InformativeDirect
Biological Process (BP)glycerophospholipid biosynthetic process0.00020450.0009882Highly InformativeDirect
Biological Process (BP)symbiosis, encompassing mutualism through parasitism0.00082180.008416Highly InformativeInherited
Biological Process (BP)multi-organism cellular process0.000063580.004713Highly InformativeInherited
Biological Process (BP)tRNA modification0.0017010.0004167Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.022960.007462Moderately InformativeInherited
Molecular Function (MF)anion binding0.045680.1399Moderately InformativeInherited
Molecular Function (MF)carbohydrate derivative binding0.0044480.03522Moderately InformativeInherited
Molecular Function (MF)cofactor binding0.0000060180.000000007788InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors0.48410.9209InformativeInherited
Molecular Function (MF)nucleotide binding0.0028150.0007956InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups0.00083760.001412InformativeInherited
Molecular Function (MF)prenyltransferase activity0.000025570.000002538Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.11381Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.17860.3824Least InformativeInherited
Cellular Component (CC)microbody0.00000000000024680.000000000001293InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) nitrogen compound metabolic process 0.00041 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0003221 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0004237 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.002989 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.06782 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01537 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00000000003292 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.00003843 Moderately Informative Direct
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.04653 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.9403 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.01871 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.3748 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.00143 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.06022 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.5705 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.07407 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.8613 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.4293 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.1026 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6169 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.2744 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.07089 Moderately Informative Inherited
Biological Process (BP) gene expression 0.8036 Moderately Informative Inherited
Biological Process (BP) RNA modification 0.00000005961 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0001392 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00006294 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.06087 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.1821 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.8324 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1791 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.04858 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.4479 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.136 Informative Inherited
Biological Process (BP) RNA processing 0.0111 Informative Inherited
Biological Process (BP) lactate metabolic process 0.00004544 Highly Informative Direct
Biological Process (BP) tRNA modification 0.0004167 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) photorespiration 0.0000000006945 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 0.00006311 Highly Informative Direct
Biological Process (BP) glycerophospholipid biosynthetic process 0.0009882 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.008416 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.004713 Highly Informative Inherited
Biological Process (BP) glutamate metabolic process 0.002567 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1399 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.03522 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.007462 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0007956 Informative Direct
Molecular Function (MF) cofactor binding 0.000000007788 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.9209 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.001412 Informative Inherited
Molecular Function (MF) prenyltransferase activity 0.000002538 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0 Highly Informative Direct
Molecular Function (MF) NADP binding 0.0002242 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3824 Least Informative Inherited
Cellular Component (CC) microbody 0.000000000001293 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-CH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH1Moderately InformativeInherited
Enzyme Commission (EC)Transposing C==C bonds0InformativeDirect
Enzyme Commission (EC)With other acceptors0.0000000000001427InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00008571InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADH)0.0000001803Highly InformativeDirect
Enzyme Commission (EC)Dihydropyrimidine dehydrogenase (NADP(+))0.0000008676Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADPH)0.00000537Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-OH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0.7933InformativeInherited
Enzyme Commission (EC)Acting on single donors with incorporation of molecular oxygen1InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH1InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)With a quinone or related compound as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Transposing C==C bonds0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000005522Highly InformativeDirect
Enzyme Commission (EC)[Acyl-carrier-protein] S-malonyltransferase0.00004073Highly InformativeDirect
Enzyme Commission (EC)With incorporation of one atom of oxygen0.00005055Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0Moderately InformativeDirect
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processtRNA processing0InformativeDirect
Biological processLipid biosynthesis0.000000000000003003InformativeDirect
Biological processDetoxification0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeroxisome0.0000000000007469InformativeDirect
DomainGlutamine amidotransferase0.0000213Highly InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0.00000002155Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.0000000000005454Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.00002553Moderately InformativeDirect
UniPathway (UP)energy metabolism0.2128Moderately InformativeInherited
UniPathway (UP)fatty acid metabolism1Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)L-glutamate metabolism0InformativeDirect
UniPathway (UP)organic acid biosynthesis0.00000000001337InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.03161InformativeInherited
UniPathway (UP)nonprotein amino-acid biosynthesis0.2593InformativeInherited
UniPathway (UP)organic acid degradation1InformativeInherited
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-glutamate biosynthesis0Highly InformativeDirect
UniPathway (UP)glycerophospholipid metabolism0Highly InformativeDirect
UniPathway (UP)oxylipin biosynthesis0.00000001087Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 28 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a FMN-linked oxidoreductases domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 28 hidden Markov models representing the FMN-linked oxidoreductases superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]