SUPERFAMILY 1.75 HMM library and genome assignments server

Ribulose-phoshate binding barrel superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   Ribulose-phoshate binding barrel [ 51366] (6)
Families:   Histidine biosynthesis enzymes [ 51367] (2)
  D-ribulose-5-phosphate 3-epimerase [ 51372]
  Decarboxylase [ 51375] (3)
  Tryptophan biosynthesis enzymes [ 51381] (3)
  NanE-like [ 117362]
  PdxS-like [ 141755]


Superfamily statistics
Genomes (3,185) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 24,316 145,831 73
Proteins 23,571 141,626 72


Functional annotation
General category Metabolism
Detailed category Nucleotide 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)cellular aromatic compound metabolic process0.00000000000010390Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.0000000000065020Least InformativeDirect
Biological Process (BP)biosynthetic process0.000024830.00000000001215Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.0000000000000032510Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000071450.0000004451Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.0000000000026130Least InformativeDirect
Biological Process (BP)cellular amino acid metabolic process0.000028720.00000000000002089Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process0.00000059490.00000002743Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.000000000010850Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000000058110.0000000000002404Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.00053870.00002249Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.000000037070.00000000000002089Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.00022120.0000001139Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.0001040.00001937Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.000000095590.000000000000007248Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000000000076170Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.00000000048530Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.25610.2535Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.28040.2646Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.00062440.00222Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.66110.2309Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.0071230.03963Moderately InformativeInherited
Biological Process (BP)oxidation-reduction process0.010540.02796Moderately InformativeInherited
Biological Process (BP)cellular biogenic amine metabolic process0.00000000027520InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.0000007780.000008305InformativeDirect
Biological Process (BP)vitamin metabolic process0.0002250.0001584InformativeDirect
Biological Process (BP)carbohydrate catabolic process0.0000000000070550.0000000000004126InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.0002540.00000001041InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process00InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00027460.0000000000001008InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.00000049930.00000000256InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.068820.0006975InformativeInherited
Biological Process (BP)hexose metabolic process0.037230.1019InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.67930.06234InformativeInherited
Biological Process (BP)nucleoside monophosphate metabolic process0.79371InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.0030390.02313InformativeInherited
Biological Process (BP)tryptophan metabolic process0.0004130.0000000001567Highly InformativeDirect
Biological Process (BP)aromatic amino acid family biosynthetic process0.000000041330Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process00Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.0000003340Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process00Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.00000041310.000000000000001913Highly InformativeDirect
Biological Process (BP)monosaccharide catabolic process00.00000001361Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process00Highly InformativeDirect
Biological Process (BP)imidazole-containing compound metabolic process0.0000000044440.00000000000003082Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.0000015850.00000005318Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.0047610.0000007531Highly InformativeInherited
Biological Process (BP)pyrimidine nucleotide metabolic process0.023350.000001471Highly InformativeInherited
Biological Process (BP)nucleoside monophosphate biosynthetic process0.001930.00000156Highly InformativeInherited
Biological Process (BP)glucose metabolic process0.087290.1108Highly InformativeInherited
Molecular Function (MF)lyase activity0.000000028310Moderately InformativeDirect
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.000073470.0000000006399InformativeDirect
Molecular Function (MF)hydro-lyase activity0.00096580.0000003735InformativeDirect
Molecular Function (MF)racemase and epimerase activity0.000012240.000002595InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.52390.05335InformativeInherited
Molecular Function (MF)racemase and epimerase activity, acting on carbohydrates and derivatives00Highly InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity, interconverting aldoses and ketoses00Highly InformativeDirect
Molecular Function (MF)carboxy-lyase activity0.00013730.001289Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.25670.0159Least InformativeInherited
Cellular Component (CC)plastid0.0024960.0000007159InformativeInherited

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 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00000000001215 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000004451 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.00000000000002089 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.00000002743 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000000000002404 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.00002249 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.00000000000002089 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.0000001139 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00001937 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.000000000000007248 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.2535 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2646 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.00222 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.2309 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.03963 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.02796 Moderately Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 0 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.000008305 Informative Direct
Biological Process (BP) vitamin metabolic process 0.0001584 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.0000000000004126 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00000001041 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.0000000000001008 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.00000000256 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.0006975 Informative Direct
Biological Process (BP) hexose metabolic process 0.1019 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.06234 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 1 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.02313 Informative Inherited
Biological Process (BP) pyrimidine nucleotide metabolic process 0.000001471 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 0.0000000001567 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.0000007531 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 0.00000156 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.000000000000001913 Highly Informative Direct
Biological Process (BP) monosaccharide catabolic process 0.00000001361 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0.00000000000003082 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.00000005318 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.1108 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring glycosyl groups 0.0000000003336 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000000006399 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0000003735 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.000002595 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.05335 Informative Inherited
Molecular Function (MF) transferase activity, transferring pentosyl groups 0 Highly Informative Direct
Molecular Function (MF) racemase and epimerase activity, acting on carbohydrates and derivatives 0 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.001289 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0159 Least Informative Inherited
Cellular Component (CC) plastid 0.0000007159 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)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Racemases and epimerases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related c0InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases1InformativeInherited
Enzyme Commission (EC)Aldehyde-lyases1InformativeInherited
Enzyme Commission (EC)Anthranilate synthase0.0000000009889Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least 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.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four 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)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases1InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0Highly InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related compounds0Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases1Highly InformativeInherited
Enzyme Commission (EC)Oxo-acid-lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processAromatic amino acid biosynthesis0Highly InformativeDirect
Biological processHistidine biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Molecular functionCobalt0.0000000002112InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
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)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0.0003343Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis1Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)one-carbon metabolism1Moderately InformativeInherited
UniPathway (UP)L-histidine biosynthesis0InformativeDirect
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)amino-sugar metabolism0InformativeDirect
UniPathway (UP)tryptophan metabolism0InformativeDirect
UniPathway (UP)amine and polyamine degradation0InformativeDirect
UniPathway (UP)aromatic amino-acid biosynthesis0InformativeDirect
UniPathway (UP)L-tryptophan biosynthesis0Highly InformativeDirect
UniPathway (UP)N-acetylneuraminate degradation0Highly InformativeDirect
UniPathway (UP)L-ascorbate degradation0.0001334Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011060 SSF51366 Protein matches
Abstract

The ribulose-phosphate binding barrel consists of a parallel beta-sheet barrel fold containing a phosphate-binding site. Several proteins display this fold, including histidine biosynthesis enzymes, tryptophan biosynthesis enzymes, D-ribulose-5-phosphate 3-epimerase, and decarboxylases [PubMed11688714].


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) · 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 36 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 Ribulose-phoshate binding barrel 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 36 hidden Markov models representing the Ribulose-phoshate binding barrel 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]