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 (3,169) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 28,305 145,394 53
Proteins 28,111 145,265 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)regulation of metabolic process11Least InformativeInherited
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.0020980.003963Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.22220.06622Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.20350.0004135Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.024390.0003963Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.10120.01486Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.35391.248e-07Least InformativeInherited
Biological Process (BP)lipid metabolic process0.049390.05504Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.8881Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.23750.9169Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.31020.6257Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.21320.579Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0042254.75e-05Moderately InformativeInherited
Biological Process (BP)multi-organism process0.05020.4179Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.55751Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.94760.3838Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.0072250.1089Moderately InformativeInherited
Biological Process (BP)gene expression0.055820.7278Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0045770.4144Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.059380.2863Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.037146.094e-07Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.052220.05263Moderately InformativeInherited
Biological Process (BP)RNA modification1.927e-075.709e-08InformativeDirect
Biological Process (BP)ncRNA metabolic process2.477e-050.0001347InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process1.088e-080InformativeDirect
Biological Process (BP)phospholipid metabolic process0.0080480.05957InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.011760.1812InformativeInherited
Biological Process (BP)RNA processing0.00012120.01085InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0037164.608e-05InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.27210.4851InformativeInherited
Biological Process (BP)lactate metabolic process0.00077463.756e-05Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process3.226e-100Highly InformativeDirect
Biological Process (BP)photorespiration2.875e-086.91e-10Highly InformativeDirect
Biological Process (BP)glycerophospholipid biosynthetic process0.00020680.0009592Highly InformativeDirect
Biological Process (BP)interaction with host2.969e-050.0005114Highly InformativeDirect
Biological Process (BP)modification of morphology or physiology of other organism involved in symbiotic interaction1.548e-063.869e-05Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process1.405e-112.04e-13Highly InformativeDirect
Biological Process (BP)multi-organism cellular process5.573e-050.003502Highly InformativeInherited
Biological Process (BP)tRNA modification0.0017170.0004021Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding0.045470.1376Moderately InformativeInherited
Molecular Function (MF)cofactor binding6.02e-067.488e-09InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors0.48540.9224InformativeInherited
Molecular Function (MF)nucleotide binding0.0028190.0007738InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups0.00083440.001386InformativeInherited
Molecular Function (MF)prenyltransferase activity2.548e-052.478e-06Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.15531Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.19030.3632Least InformativeInherited
Cellular Component (CC)microbody2.508e-131.275e-12InformativeDirect

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 0.0004135 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1.248e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0003963 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.06622 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 0.003963 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01486 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 6.094e-07 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 4.75e-05 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.05504 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.9169 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.06468 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.01986 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6257 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.579 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4179 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1089 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.3838 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.1106 Moderately Informative Inherited
Biological Process (BP) gene expression 0.7278 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.4144 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.3311 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.2863 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.05263 Moderately Informative Inherited
Biological Process (BP) RNA modification 5.709e-08 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0001347 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 4.608e-05 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.05957 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.1812 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.8533 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1945 Informative Inherited
Biological Process (BP) RNA processing 0.01085 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.4851 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.1445 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.05757 Informative Inherited
Biological Process (BP) lactate metabolic process 3.756e-05 Highly Informative Direct
Biological Process (BP) tRNA modification 0.0004021 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) photorespiration 6.91e-10 Highly Informative Direct
Biological Process (BP) glycerophospholipid biosynthetic process 0.0009592 Highly Informative Direct
Biological Process (BP) interaction with host 0.0005114 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 3.869e-05 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 2.04e-13 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.003502 Highly Informative Inherited
Biological Process (BP) glutamate metabolic process 0.002558 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1376 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0007738 Informative Direct
Molecular Function (MF) cofactor binding 7.488e-09 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.9224 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.001386 Informative Inherited
Molecular Function (MF) prenyltransferase activity 2.478e-06 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 0.0002211 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3632 Least Informative Inherited
Cellular Component (CC) microbody 1.275e-12 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)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 acceptor5.522e-08Highly InformativeDirect
Enzyme Commission (EC)[Acyl-carrier-protein] S-malonyltransferase4.073e-05Highly InformativeDirect
Enzyme Commission (EC)With incorporation of one atom of oxygen5.055e-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 biosynthesis3.003e-15InformativeDirect
Biological processDetoxification0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeroxisome7.469e-13InformativeDirect
DomainGlutamine amidotransferase2.13e-05Highly 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 metabolism2.155e-08Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism5.454e-13Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism2.553e-05Moderately 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 biosynthesis1.337e-11InformativeDirect
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 biosynthesis1.087e-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 ]