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Riboflavin synthase domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Reductase/isomerase/elongation factor common domain [ 50412] (4)
Superfamily:   Riboflavin synthase domain-like [ 63380] (3)
Families:   Riboflavin synthase [ 63783]
  Ferredoxin reductase FAD-binding domain-like [ 63381] (9)
  NADPH-cytochrome p450 reductase FAD-binding domain-like [ 50438] (3)


Superfamily statistics
Genomes (3,025) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 25,880 132,753 62
Proteins 23,267 117,793 60


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0.00000000000002769 Least Informative Direct
Biological Process (BP) response to stimulus 0.00004965 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.7063 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2843 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.2431 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.01559 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0.0000000000003337 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.000000009799 Moderately Informative Direct
Biological Process (BP) response to biotic stimulus 0.0000001004 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0000002746 Moderately Informative Direct
Biological Process (BP) defense response 0.00001533 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.0001103 Moderately Informative Direct
Biological Process (BP) ion transport 0.0001943 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.2902 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.7357 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.9374 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.8567 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.0228 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.09467 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.05589 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3827 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.3504 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.004259 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.05397 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.8195 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.2261 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.4722 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.3253 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.1507 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.009815 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2654 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.9719 Moderately Informative Inherited
Biological Process (BP) cell communication 0.6877 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.9497 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.06689 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.2856 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.02534 Moderately Informative Inherited
Biological Process (BP) electron transport chain 0.00002627 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 0.00008455 Informative Direct
Biological Process (BP) lipid localization 0.0001345 Informative Direct
Biological Process (BP) secretion by cell 0.0002067 Informative Direct
Biological Process (BP) organic acid transport 0.000564 Informative Direct
Biological Process (BP) alcohol metabolic process 0.8478 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.09089 Informative Inherited
Biological Process (BP) regulation of defense response 0.09713 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.001112 Informative Inherited
Biological Process (BP) protein transport 0.1978 Informative Inherited
Biological Process (BP) anion transport 0.08797 Informative Inherited
Biological Process (BP) cellular response to inorganic substance 0.06427 Informative Inherited
Biological Process (BP) response to metal ion 0.1293 Informative Inherited
Biological Process (BP) cation homeostasis 0.002856 Informative Inherited
Biological Process (BP) inorganic ion homeostasis 0.00328 Informative Inherited
Biological Process (BP) cellular chemical homeostasis 0.3362 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.01906 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.2518 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.5837 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.1864 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.002175 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.016 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.01642 Informative Inherited
Biological Process (BP) water-soluble vitamin biosynthetic process 0.8427 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.1589 Informative Inherited
Biological Process (BP) ribose phosphate biosynthetic process 0.006449 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.3846 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.1187 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) metal ion transport 0.07237 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.05332 Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.05332 Informative Inherited
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.003774 Informative Inherited
Biological Process (BP) system process 0.5374 Informative Inherited
Biological Process (BP) behavior 0.2911 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.1016 Informative Inherited
Biological Process (BP) response to purine-containing compound 0.0000000000003023 Highly Informative Direct
Biological Process (BP) response to organophosphorus 0.00000000000149 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0.00000003115 Highly Informative Direct
Biological Process (BP) protein secretion 0.00000008163 Highly Informative Direct
Biological Process (BP) monocarboxylic acid transport 0.0000001228 Highly Informative Direct
Biological Process (BP) arginine metabolic process 0.0000007984 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleotide metabolic process 0.0000009219 Highly Informative Direct
Biological Process (BP) pyrimidine nucleotide biosynthetic process 0.000002107 Highly Informative Direct
Biological Process (BP) glutamine family amino acid catabolic process 0.000004619 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.00002803 Highly Informative Direct
Biological Process (BP) phenol-containing compound metabolic process 0.00004925 Highly Informative Direct
Biological Process (BP) secondary alcohol metabolic process 0.0001382 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 0.000278 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.0004692 Highly Informative Direct
Biological Process (BP) transition metal ion transport 0.0007933 Highly Informative Direct
Biological Process (BP) hydrogen peroxide metabolic process 1 Highly Informative Inherited
Biological Process (BP) response to ketone 0.004568 Highly Informative Inherited
Biological Process (BP) response to carbohydrate 0.0398 Highly Informative Inherited
Biological Process (BP) aging 0.009866 Highly Informative Inherited
Biological Process (BP) second-messenger-mediated signaling 0.003119 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00002902 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.001737 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) tetrapyrrole binding 0.00000000000000853 Informative Direct
Molecular Function (MF) electron carrier activity 0.00000004919 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.00005321 Informative Direct
Molecular Function (MF) ribonucleotide binding 1 Informative Inherited
Molecular Function (MF) heme binding 0 Highly Informative Direct
Molecular Function (MF) FMN binding 0 Highly Informative Direct
Molecular Function (MF) NADP binding 0.00000000000008835 Highly Informative Direct
Molecular Function (MF) iron-sulfur cluster binding 0.00006981 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on iron-sulfur proteins as donors 0.001265 Highly Informative Inherited
Molecular Function (MF) monooxygenase activity 0.02149 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.002577 Highly Informative Inherited
Molecular Function (MF) dioxygenase activity 0.7739 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.7314 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 1 Highly Informative Inherited
Cellular Component (CC) membrane 0.04605 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.485 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.01276 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.3565 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.001119 Moderately Informative Inherited
Cellular Component (CC) oxidoreductase complex 0.000000000008369 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0004559 Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.01577 Highly Informative Inherited

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)Acting on NADH or NADPH0Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)Acting on a sulfur group of donors0.000000000000007826Moderately InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0.00000000001461InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation0.06286InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Sulfite reductase (NADPH)0Highly InformativeDirect
Enzyme Commission (EC)Nitric-oxide synthase0Highly InformativeDirect
Enzyme Commission (EC)With a heme protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Nitrate reductase (NADH)0Highly InformativeDirect
Enzyme Commission (EC)Nitric oxide dioxygenase0.000000000001117Highly InformativeDirect
Enzyme Commission (EC)Nitrate reductase (NADPH)0.0000000004944Highly InformativeDirect
Enzyme Commission (EC)With a oxygen as acceptor0.000000004206Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processLipid metabolism0.0003773Moderately InformativeDirect
Biological processAmino-acid biosynthesis0.0004451Moderately InformativeDirect
Biological processIon transport0.6308Moderately InformativeInherited
Biological processAromatic hydrocarbons catabolism0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processSteroid metabolism0InformativeDirect
Biological processLipid biosynthesis0.002334InformativeInherited
Biological processSodium transport0Highly InformativeDirect
Biological processLuminescence0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processDetoxification0Highly InformativeDirect
Biological processCysteine biosynthesis0Highly InformativeDirect
Biological processNitrate assimilation0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processOxygen transport4.848e-16Highly InformativeDirect
Biological processSterol biosynthesis0.000000238Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentMitochondrion outer membrane0InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionMetal-binding0.00001067Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Molecular functionCalcium0.0001621Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionSodium0InformativeDirect
Molecular functionHeme0InformativeDirect
Molecular functionMolybdenum0InformativeDirect
Molecular functionFAD0InformativeDirect
Molecular functionUbiquinone0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationCalmodulin-binding0InformativeDirect
Post-translational modificationIon channel0.01915InformativeInherited
Post-translational modificationVoltage-gated channel0.000707Highly InformativeDirect
Post-translational modificationMyristate0.0000004313InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 26 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 Riboflavin synthase domain-like 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 26 hidden Markov models representing the Riboflavin synthase domain-like 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]