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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 (2,463) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 6,767 21,363 10
Proteins 6,751 21,346 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 process0.12550.2041Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.067970.1265Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.22440.1442Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.042590.07747Least InformativeInherited
Biological Process (BP)biosynthetic process0.18340.2707Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.0027990.001854Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.003270.002342Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.0048020.004644Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0057530.000816Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.0089090.003637Moderately InformativeInherited
Biological Process (BP)vitamin metabolic process4.639e-061.776e-08InformativeDirect
Molecular Function (MF)lyase activity1.198e-053.2e-06Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity4.887e-081.66e-09InformativeDirect

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 0.2041 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1265 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1442 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.07747 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.2707 Least Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.000816 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.001854 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.002342 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.004644 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.003637 Moderately Informative Inherited
Biological Process (BP) vitamin metabolic process 1.776e-08 Informative Direct
Molecular Function (MF) lyase activity 3.2e-06 Moderately Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 1.66e-09 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)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases7.788e-07Least 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 amidines0Highly InformativeDirect
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 functionZinc1.957e-08Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Molecular functionGTP-binding2.517e-13InformativeDirect
Post-translational modificationHydrolase0.000345Least InformativeDirect
Post-translational modificationLyase0Moderately 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)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 ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.