SUPERFAMILY 1.75 HMM library and genome assignments server


Homo-oligomeric flavin-containing Cys decarboxylases, HFCD superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [ 52506]
Superfamily:   Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [ 52507]
Families:   Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [ 52508] (4)


Superfamily statistics
Genomes (2,981) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 5,426 12,963 7
Proteins 5,393 12,930 7


Functional annotation
General category Metabolism
Detailed category Secondary metabolism

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)biosynthetic process4.697e-063.614e-06Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.19930.003548Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.094950.02329Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.15450.002014Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.19350.04286Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.007076.076e-06Least InformativeInherited
Biological Process (BP)cofactor metabolic process4.318e-073.865e-12Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process0.0026126.986e-05Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0023521.001e-06Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0033391.729e-06Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.032596.746e-05Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.020010.0003926Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0042264.382e-06Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.022010.000477Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0056736.118e-07Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.0051811.22e-05Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process3.421e-110InformativeDirect
Biological Process (BP)purine ribonucleotide metabolic process3.565e-061.37e-09InformativeDirect
Biological Process (BP)nucleotide biosynthetic process1.807e-071.431e-14InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process4.735e-067.356e-10InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process4.585e-091.765e-09InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process6.411e-061.603e-10InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process3.669e-051.805e-11InformativeDirect
Biological Process (BP)purine ribonucleotide biosynthetic process1.392e-090Highly InformativeDirect
Biological Process (BP)coenzyme A metabolic process2.595e-070Highly InformativeDirect
Biological Process (BP)ribonucleoside bisphosphate biosynthetic process7.574e-130Highly InformativeDirect
Biological Process (BP)purine nucleoside bisphosphate biosynthetic process7.574e-130Highly InformativeDirect
Molecular Function (MF)lyase activity1.872e-090Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity3.602e-140InformativeDirect
Molecular Function (MF)carboxy-lyase activity00Highly InformativeDirect

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) biosynthetic process 3.614e-06 Least Informative Direct
Biological Process (BP) single-organism metabolic process 6.076e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.02329 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.002014 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.003548 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.04286 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 6.986e-05 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 6.746e-05 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0003926 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 1.001e-06 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 4.382e-06 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 3.865e-12 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 1.22e-05 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 1.729e-06 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000477 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 6.118e-07 Moderately Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 1.37e-09 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 1.431e-14 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 7.356e-10 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 1.765e-09 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 1.603e-10 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 1.805e-11 Informative Direct
Biological Process (BP) purine ribonucleotide biosynthetic process 0 Highly Informative Direct
Biological Process (BP) coenzyme A metabolic process 0 Highly Informative Direct
Biological Process (BP) ribonucleoside bisphosphate biosynthetic process 0 Highly Informative Direct
Biological Process (BP) purine nucleoside bisphosphate biosynthetic process 0 Highly Informative Direct
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) carboxy-lyase activity 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Ligases5.415e-07Least InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds3.428e-12Moderately InformativeDirect
Enzyme Commission (EC)Acid--D-amino-acid ligases (peptide synthases)0InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases1.392e-06Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0InformativeDirect
Enzyme Commission (EC)Acid--amino-acid ligases (peptide synthases)0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionFMN0InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)coenzyme A biosynthesis0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR003382 SSF52507 Protein matches
Abstract This entry contains a diverse range of flavoprotein enzymes, including epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN [PubMed1644762]. This enzyme catalyzes the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance [PubMed8345520]. Dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenylacrylic acid decarboxylase [PubMed8181743].

InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · 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 5 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 Homo-oligomeric flavin-containing Cys decarboxylases, HFCD 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 5 hidden Markov models representing the Homo-oligomeric flavin-containing Cys decarboxylases, HFCD 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]