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 (3,163) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 28,070 145,394 53
Proteins 27,888 145,265 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 process0.0058090.00739Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.15270.04603Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.28290.0007991Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.027650.0003449Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.06320.009165Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.32770.00000009305Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.2320.5094Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.14740.4643Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.020550.0001586Moderately InformativeInherited
Biological Process (BP)multi-organism process0.043670.4096Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.99690.4453Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.0077680.1095Moderately InformativeInherited
Biological Process (BP)gene expression0.063640.7805Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0054160.4681Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.12240.389Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.031370.0000005434Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.05210.04483Moderately InformativeInherited
Biological Process (BP)RNA modification0.00000023360.00000007691InformativeDirect
Biological Process (BP)ncRNA metabolic process0.000023520.0001671InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.000000004490InformativeDirect
Biological Process (BP)RNA processing0.00014480.01342InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0027810.0000345InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.26320.4769InformativeInherited
Biological Process (BP)lactate metabolic process0.00056530.0000336Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.00000000040070Highly InformativeDirect
Biological Process (BP)photorespiration0.000000036630.0000000009344Highly InformativeDirect
Biological Process (BP)modification of morphology or physiology of other organism0.0000033440.00005945Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.000000000014250.00000000000008856Highly InformativeDirect
Biological Process (BP)symbiosis, encompassing mutualism through parasitism0.00029920.005422Highly InformativeInherited
Biological Process (BP)multi-organism cellular process0.000066820.004092Highly InformativeInherited
Biological Process (BP)tRNA modification0.0020240.0005155Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding0.099660.2462Moderately InformativeInherited
Molecular Function (MF)cofactor binding0.000033170.00000005149InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors0.60280.9853InformativeInherited
Molecular Function (MF)nucleotide binding0.0097030.002915InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups0.00081740.001375InformativeInherited
Molecular Function (MF)prenyltransferase activity0.000027920.000002275Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.21711Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.24060.4671Least InformativeInherited
Cellular Component (CC)microbody0.00000000000036840.000000000002151InformativeDirect

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 0.0007991 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00000009305 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0003449 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.04603 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 0.00739 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.009165 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0000005434 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0001586 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.05 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.01378 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.5094 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.4643 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4096 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1095 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.4453 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.09494 Moderately Informative Inherited
Biological Process (BP) gene expression 0.7805 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.4681 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.2893 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.389 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.04483 Moderately Informative Inherited
Biological Process (BP) RNA modification 0.00000007691 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0001671 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.0000345 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.8639 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1994 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.153 Informative Inherited
Biological Process (BP) RNA processing 0.01342 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.4769 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.135 Informative Inherited
Biological Process (BP) lactate metabolic process 0.0000336 Highly Informative Direct
Biological Process (BP) tRNA modification 0.0005155 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) photorespiration 0.0000000009344 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 0.00005945 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.00000000000008856 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.005422 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.004092 Highly Informative Inherited
Biological Process (BP) glutamate metabolic process 0.002898 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 0.2462 Moderately Informative Inherited
Molecular Function (MF) cofactor binding 0.00000005149 Informative Direct
Molecular Function (MF) nucleotide binding 0.002915 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.9853 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.001375 Informative Inherited
Molecular Function (MF) prenyltransferase activity 0.000002275 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 0.00009852 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4671 Least Informative Inherited
Cellular Component (CC) microbody 0.000000000002151 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 donors0.9985InformativeInherited
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 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 acceptor0.00000004879Highly InformativeDirect
Enzyme Commission (EC)[Acyl-carrier-protein] S-malonyltransferase0.00004658Highly InformativeDirect
Enzyme Commission (EC)With incorporation of one atom of oxygen0.00005774Highly 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 biosynthesis0.000000000000003689InformativeDirect
Biological processDetoxification0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeroxisome0.0000000000001209InformativeDirect
DomainGlutamine amidotransferase0.00001967Highly InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionIron-sulfur0.000004713InformativeDirect
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 metabolism0.00000001751Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.0000000000005145Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.0000247Moderately InformativeDirect
UniPathway (UP)energy metabolism0.2097Moderately 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 biosynthesis0.00000000001226InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.03163InformativeInherited
UniPathway (UP)nonprotein amino-acid biosynthesis0.2588InformativeInherited
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 ]