SUPERFAMILY 1.75 HMM library and genome assignments server


YrdC/RibB superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   YrdC/RibB [ 55820]
Superfamily:   YrdC/RibB [ 55821] (2)
Families:   YrdC-like [ 55822] (3)
  3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB [ 64372]


Superfamily statistics
Genomes (3,204) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,712 49,090 10
Proteins 8,698 49,069 10


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

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)nitrogen compound metabolic process0.13280.1846Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.073820.1088Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.22450.1436Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.047370.06361Least InformativeInherited
Biological Process (BP)biosynthetic process0.17960.4855Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.0032290.007611Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0029530.007455Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.0056680.01686Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0056520.003732Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.0050840.002432Moderately InformativeInherited
Biological Process (BP)vitamin metabolic process6.86e-061.842e-07InformativeDirect
Molecular Function (MF)lyase activity1.367e-051.356e-06Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity5.25e-082.276e-10InformativeDirect

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 0.1846 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1088 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1436 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.06361 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.4855 Least Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.007611 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.007455 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.01686 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.003732 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.002432 Moderately Informative Inherited
Biological Process (BP) vitamin metabolic process 1.842e-07 Informative Direct
Molecular Function (MF) lyase activity 1.356e-06 Moderately Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 2.276e-10 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)In cyclic amidines0InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.2927Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)In cyclic amidines0InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processtRNA processing0InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc2.524e-09Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionGTP-binding2.492e-14InformativeDirect
Post-translational modificationTransferase2.202e-11Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect

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)biopolymer metabolism1Least InformativeInherited
UniPathway (UP)protein maturation0.0006778InformativeDirect
UniPathway (UP)riboflavin 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) · 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 7 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 YrdC/RibB 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 7 hidden Markov models representing the YrdC/RibB 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]