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 28,304 145,394 53
Proteins 28,110 145,265 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 process0.0028310.004984Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.18470.05577Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.23910.0005618Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.022650.0002574Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.080540.01191Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.37641.628e-07Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.25680.5349Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.16920.4927Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0084067.976e-05Moderately InformativeInherited
Biological Process (BP)multi-organism process0.045360.4047Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process10.4712Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.0068050.1096Moderately InformativeInherited
Biological Process (BP)gene expression0.059750.756Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0050870.4425Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.080480.3076Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.03195.357e-07Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.048440.04839Moderately InformativeInherited
Biological Process (BP)RNA modification2.126e-077.079e-08InformativeDirect
Biological Process (BP)ncRNA metabolic process2.647e-050.0001605InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process6.961e-090InformativeDirect
Biological Process (BP)RNA processing0.00014160.01234InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0032684.01e-05InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.26770.4826InformativeInherited
Biological Process (BP)lactate metabolic process0.00078673.856e-05Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process3.47e-100Highly InformativeDirect
Biological Process (BP)photorespiration3.178e-088.119e-10Highly InformativeDirect
Biological Process (BP)modification of morphology or physiology of other organism3.744e-065.685e-05Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process1.11e-111.398e-13Highly InformativeDirect
Biological Process (BP)symbiosis, encompassing mutualism through parasitism0.00056360.006389Highly InformativeInherited
Biological Process (BP)multi-organism cellular process6.073e-050.003747Highly InformativeInherited
Biological Process (BP)tRNA modification0.0016350.00039Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding0.044590.1416Moderately InformativeInherited
Molecular Function (MF)cofactor binding4.523e-065.44e-09InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors0.50570.9266InformativeInherited
Molecular Function (MF)nucleotide binding0.0027740.0008744InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups0.00076920.00132InformativeInherited
Molecular Function (MF)prenyltransferase activity2.612e-052.272e-06Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.17941Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.21430.4301Least InformativeInherited
Cellular Component (CC)microbody2.965e-131.772e-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 0.0005618 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1.628e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0002574 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.05577 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 0.004984 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01191 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 5.357e-07 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 7.976e-05 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.05696 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.5349 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.4927 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4047 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1096 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.4712 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.1023 Moderately Informative Inherited
Biological Process (BP) gene expression 0.756 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.4425 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.04974 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.006967 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.3017 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.3076 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.04839 Moderately Informative Inherited
Biological Process (BP) RNA modification 7.079e-08 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0001605 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 4.01e-05 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.8486 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.194 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.1474 Informative Inherited
Biological Process (BP) RNA processing 0.01234 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.4826 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.1343 Informative Inherited
Biological Process (BP) lactate metabolic process 3.856e-05 Highly Informative Direct
Biological Process (BP) tRNA modification 0.00039 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) photorespiration 8.119e-10 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 5.685e-05 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 1.398e-13 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.006389 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.003747 Highly Informative Inherited
Biological Process (BP) glutamate metabolic process 0.002931 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 0.1416 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0008744 Informative Direct
Molecular Function (MF) cofactor binding 5.44e-09 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.9266 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.00132 Informative Inherited
Molecular Function (MF) prenyltransferase activity 2.272e-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 0.0001589 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4301 Least Informative Inherited
Cellular Component (CC) microbody 1.772e-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 single donors with incorporation of molecular oxygen1InformativeInherited
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 acceptor5.89e-08Highly InformativeDirect
Enzyme Commission (EC)[Acyl-carrier-protein] S-malonyltransferase4.66e-05Highly InformativeDirect
Enzyme Commission (EC)With incorporation of one atom of oxygen5.776e-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 biosynthesis3.233e-15InformativeDirect
Biological processDetoxification0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeroxisome1.186e-13InformativeDirect
DomainGlutamine amidotransferase2.068e-05Highly InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionIron-sulfur5.095e-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 metabolism2.018e-08Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism5.324e-13Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism2.42e-05Moderately 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 biosynthesis1.333e-11InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.03152InformativeInherited
UniPathway (UP)nonprotein amino-acid biosynthesis0.2583InformativeInherited
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 biosynthesis1.076e-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 ]