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 (3,128) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 27,366 60,992 53
Proteins 27,252 60,906 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)regulation of metabolic process11Least InformativeInherited
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.006130.0139Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.28290.112Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.4480.003217Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.022320.000893Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.13770.02837Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.28641.016e-07Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.88781Moderately InformativeInherited
Biological Process (BP)lipid biosynthetic process0.10810.1394Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.24260.9664Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.1450.1079Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.27920.6876Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.18280.6355Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.019420.0006537Moderately InformativeInherited
Biological Process (BP)multi-organism process0.020880.2774Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.99980.4324Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.0035010.1111Moderately InformativeInherited
Biological Process (BP)gene expression0.06460.7561Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.00660.4704Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.15160.5536Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.050062.126e-06Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.033240.04114Moderately InformativeInherited
Biological Process (BP)RNA modification8.873e-083.404e-08InformativeDirect
Biological Process (BP)ncRNA metabolic process6.435e-050.000282InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process1.662e-080InformativeDirect
Biological Process (BP)phospholipid metabolic process0.0057510.05216InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.012510.1877InformativeInherited
Biological Process (BP)RNA processing0.00026330.01754InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0025312.984e-05InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.25610.4526InformativeInherited
Biological Process (BP)lactate metabolic process0.00035891.739e-05Highly InformativeDirect
Biological Process (BP)tRNA modification0.00035727.889e-05Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process2.345e-090Highly InformativeDirect
Biological Process (BP)photorespiration1.997e-085.971e-10Highly InformativeDirect
Biological Process (BP)glycerophospholipid biosynthetic process0.00015010.000828Highly InformativeDirect
Biological Process (BP)interaction with host2.898e-060.0001299Highly InformativeDirect
Biological Process (BP)modification of morphology or physiology of other organism involved in symbiotic interaction3.671e-072.101e-05Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process5.355e-115.834e-12Highly InformativeDirect
Biological Process (BP)multi-organism cellular process3.999e-050.002576Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding0.11560.2549Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups0.00046420.0009301InformativeDirect
Molecular Function (MF)cofactor binding7.173e-051.377e-07InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors0.56170.9506InformativeInherited
Molecular Function (MF)nucleotide binding0.013560.003278InformativeInherited
Molecular Function (MF)prenyltransferase activity1.362e-051.5e-06Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors6.726e-160Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.024351Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.050590.1216Least InformativeInherited
Cellular Component (CC)microbody7.355e-146.53e-13InformativeDirect

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) single-organism metabolic process 1.016e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000893 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.003217 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.112 Least Informative Inherited
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 0.0139 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.02837 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 2.126e-06 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0006537 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.1394 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.9664 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.1079 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.04123 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6876 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.6355 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2774 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1111 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.4324 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.08465 Moderately Informative Inherited
Biological Process (BP) gene expression 0.7561 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.4704 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.02864 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.004056 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.3695 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.5536 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.04114 Moderately Informative Inherited
Biological Process (BP) RNA modification 3.404e-08 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.000282 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 2.984e-05 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.05216 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.1877 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.7727 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1668 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.1228 Informative Inherited
Biological Process (BP) RNA processing 0.01754 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.4526 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.1353 Informative Inherited
Biological Process (BP) lactate metabolic process 1.739e-05 Highly Informative Direct
Biological Process (BP) tRNA modification 7.889e-05 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) photorespiration 5.971e-10 Highly Informative Direct
Biological Process (BP) glycerophospholipid biosynthetic process 0.000828 Highly Informative Direct
Biological Process (BP) interaction with host 0.0001299 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 2.101e-05 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 5.834e-12 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.002576 Highly Informative Inherited
Biological Process (BP) glutamate metabolic process 0.003046 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.2549 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.0009301 Informative Direct
Molecular Function (MF) cofactor binding 1.377e-07 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.9506 Informative Inherited
Molecular Function (MF) nucleotide binding 0.003278 Informative Inherited
Molecular Function (MF) prenyltransferase activity 1.5e-06 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1216 Least Informative Inherited
Cellular Component (CC) microbody 6.53e-13 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 acceptors1.427e-13InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor8.571e-05InformativeDirect
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)1.803e-07Highly InformativeDirect
Enzyme Commission (EC)Dihydropyrimidine dehydrogenase (NADP(+))8.676e-07Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADPH)5.37e-06Highly 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)fertile0Least 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)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors1InformativeInherited
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 cytochrome as acceptor0Highly InformativeDirect
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 acceptor5.151e-08Highly InformativeDirect
Enzyme Commission (EC)[Acyl-carrier-protein] S-malonyltransferase4.838e-05Highly 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 biosynthesis4.148e-15InformativeDirect
Biological processDetoxification0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeroxisome1.47e-13InformativeDirect
DomainGlutamine amidotransferase2.131e-05Highly InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionIron-sulfur5.167e-06InformativeDirect
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 metabolism1.838e-08Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism1.683e-12Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism2.388e-05Moderately InformativeDirect
UniPathway (UP)energy metabolism0.2113Moderately InformativeInherited
UniPathway (UP)fatty acid metabolism1Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)organic acid biosynthesis5.212e-12InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.02762InformativeInherited
UniPathway (UP)nonprotein amino-acid biosynthesis0.26InformativeInherited
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 biosynthesis1.091e-08Highly 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 ]