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 (3,022) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,410 28,203 7
Proteins 5,377 28,154 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 process0.00000084870.0000004581Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.00081570.00003992Least InformativeDirect
Biological Process (BP)single-organism cellular process0.18340.2121Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.09020.0005356Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.11850.01456Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.055630.00772Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.12160.0009512Least InformativeInherited
Biological Process (BP)response to stimulus0.39641Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.00059550.000005753Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.00066220.00000004939Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.000000080920.0000000000000325Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.000037490.000000000275Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.0020760.00000003963Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.0073720.00005456Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0010230.0000001067Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.0019190.002345Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0015390.0000004314Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.0083680.00007117Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.013240.000007795Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.0000000000017560InformativeDirect
Biological Process (BP)purine ribonucleotide metabolic process0.00000031110.00000000001197InformativeDirect
Biological Process (BP)nucleotide biosynthetic process0.0000000057790InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.00000044470.000000000006261InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.000000000063940.00000000002544InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.00000049440.000000000001035InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.0000035510.0000000000000567InformativeDirect
Biological Process (BP)response to salt stress0.0000039960.0000003839Highly InformativeDirect
Biological Process (BP)coenzyme A metabolic process0.000000014950Highly InformativeDirect
Biological Process (BP)ribonucleoside bisphosphate biosynthetic process0.0000000000000032510Highly InformativeDirect
Biological Process (BP)purine nucleoside bisphosphate biosynthetic process0.0000000000000032510Highly InformativeDirect
Molecular Function (MF)lyase activity0.00000000021120Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity6.814e-160InformativeDirect
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) cellular aromatic compound metabolic process 0.0009512 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0000004581 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00003992 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0005356 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.2121 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01456 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.00772 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.000005753 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000007795 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.00005456 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.00000004939 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0000004314 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0000000000000325 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.000000000275 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0000001067 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00007117 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.00000003963 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.002345 Moderately Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.00000000001197 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.000000000006261 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00000000002544 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.000000000001035 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.0000000000000567 Informative Direct
Biological Process (BP) response to salt stress 0.0000003839 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)Ligases0.0000005415Least InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds0.000000000003428Moderately 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)Ligases0.000002568Moderately 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 metabolism6.774e-16Least InformativeDirect
UniPathway (UP)coenzyme A biosynthesis0Highly InformativeDirect

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 ]