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 process0.0061550.01375Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.28430.1118Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.44830.003191Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.022660.0008853Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.13890.02836Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.28821.006e-07Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.89061Moderately InformativeInherited
Biological Process (BP)lipid biosynthetic process0.10790.1395Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.24770.9676Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.14440.1074Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.2810.6882Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.18350.6356Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.01970.0006548Moderately InformativeInherited
Biological Process (BP)multi-organism process0.020850.2791Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.99910.4314Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.0035610.1111Moderately InformativeInherited
Biological Process (BP)gene expression0.064280.7558Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0065560.4699Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.15280.5542Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.051832.221e-06Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.033360.04075Moderately InformativeInherited
Biological Process (BP)RNA modification8.793e-083.422e-08InformativeDirect
Biological Process (BP)ncRNA metabolic process6.446e-050.0002801InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process1.631e-080InformativeDirect
Biological Process (BP)phospholipid metabolic process0.0057280.05201InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.012460.1872InformativeInherited
Biological Process (BP)RNA processing0.00026130.01749InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0025052.966e-05InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.25650.454InformativeInherited
Biological Process (BP)lactate metabolic process0.00035631.733e-05Highly InformativeDirect
Biological Process (BP)tRNA modification0.00035757.787e-05Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process2.328e-090Highly InformativeDirect
Biological Process (BP)photorespiration1.986e-085.936e-10Highly InformativeDirect
Biological Process (BP)glycerophospholipid biosynthetic process0.00014950.0008245Highly InformativeDirect
Biological Process (BP)interaction with host2.88e-060.0001304Highly InformativeDirect
Biological Process (BP)modification of morphology or physiology of other organism involved in symbiotic interaction3.652e-072.09e-05Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process5.303e-115.764e-12Highly InformativeDirect
Biological Process (BP)multi-organism cellular process3.977e-050.002581Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding0.11740.2596Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups0.00046130.0009265InformativeDirect
Molecular Function (MF)cofactor binding8.281e-051.517e-07InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors0.56040.9509InformativeInherited
Molecular Function (MF)nucleotide binding0.014080.003379InformativeInherited
Molecular Function (MF)prenyltransferase activity1.351e-051.494e-06Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors6.738e-160Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.02441Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.050380.1221Least InformativeInherited
Cellular Component (CC)microbody7.358e-146.457e-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 1.006e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0008853 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.003191 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1118 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 0.01375 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.02836 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 2.221e-06 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0006548 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.1395 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.9676 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.1074 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.04151 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6882 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.6356 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2791 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1111 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.4314 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.08416 Moderately Informative Inherited
Biological Process (BP) gene expression 0.7558 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.4699 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.02921 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.004133 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.3701 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.5542 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.04075 Moderately Informative Inherited
Biological Process (BP) RNA modification 3.422e-08 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0002801 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 2.966e-05 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.05201 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.1872 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.7736 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.168 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.1242 Informative Inherited
Biological Process (BP) RNA processing 0.01749 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.454 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.1347 Informative Inherited
Biological Process (BP) lactate metabolic process 1.733e-05 Highly Informative Direct
Biological Process (BP) tRNA modification 7.787e-05 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) photorespiration 5.936e-10 Highly Informative Direct
Biological Process (BP) glycerophospholipid biosynthetic process 0.0008245 Highly Informative Direct
Biological Process (BP) interaction with host 0.0001304 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 2.09e-05 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 5.764e-12 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.002581 Highly Informative Inherited
Biological Process (BP) glutamate metabolic process 0.003044 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 0.2596 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.0009265 Informative Direct
Molecular Function (MF) cofactor binding 1.517e-07 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.9509 Informative Inherited
Molecular Function (MF) nucleotide binding 0.003379 Informative Inherited
Molecular Function (MF) prenyltransferase activity 1.494e-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 0.1221 Least Informative Inherited
Cellular Component (CC) microbody 6.457e-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)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism0.005561Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)nitrogen metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)energy metabolism3.412e-05Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)L-glutamate metabolism0InformativeDirect
UniPathway (UP)glycerophospholipid metabolism0InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis5.799e-06InformativeDirect
UniPathway (UP)organic acid biosynthesis4.22e-05InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.0004658InformativeDirect
UniPathway (UP)organic acid degradation1InformativeInherited
UniPathway (UP)beta-alanine biosynthesis0Highly 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 ]