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 (3,184) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 24,306 145,831 73
Proteins 23,562 141,626 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 process7.46e-130Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process4.59e-110Least InformativeDirect
Biological Process (BP)biosynthetic process3.35e-052.164e-11Least InformativeDirect
Biological Process (BP)single-organism metabolic process7.41e-110Least InformativeDirect
Biological Process (BP)heterocycle metabolic process3.261e-150Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.014e-110Least InformativeDirect
Biological Process (BP)cellular amino acid metabolic process2.804e-051.953e-14Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process3.072e-074.131e-08Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process8.11e-110Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process3.05e-081.659e-12Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.00040911.624e-05Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process1.895e-071.736e-13Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process4.307e-064.668e-11Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process5.99e-051.439e-05Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process5.481e-100Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process3.6e-090Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.62340.199Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.00064680.002286Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.29510.2728Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.0025991.94e-05Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.013660.0635Moderately InformativeInherited
Biological Process (BP)cellular biogenic amine metabolic process2.792e-100InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process1.789e-061.431e-05InformativeDirect
Biological Process (BP)vitamin metabolic process0.00031620.000221InformativeDirect
Biological Process (BP)carbohydrate catabolic process7.076e-124.277e-13InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.00030451.514e-08InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process00InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00022117.357e-14InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process6.591e-073.652e-09InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.073240.0007866InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.74260.0854InformativeInherited
Biological Process (BP)nucleoside monophosphate metabolic process0.63220.9769InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.006130.0415InformativeInherited
Biological Process (BP)hexose metabolic process0.063510.1424InformativeInherited
Biological Process (BP)tryptophan metabolic process0.00038281.368e-10Highly InformativeDirect
Biological Process (BP)aromatic amino acid family biosynthetic process2.957e-080Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process00Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process2.416e-070Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process6.965e-067.307e-08Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process4.161e-071.938e-15Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process00Highly InformativeDirect
Biological Process (BP)imidazole-containing compound metabolic process4.162e-092.963e-14Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process2.765e-061.705e-07Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process3.078e-056.402e-13Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.004447.767e-07Highly InformativeInherited
Biological Process (BP)pyrimidine nucleotide metabolic process0.028562.325e-06Highly InformativeInherited
Biological Process (BP)nucleoside monophosphate biosynthetic process0.0030272.772e-06Highly InformativeInherited
Molecular Function (MF)lyase activity1.967e-080Moderately InformativeDirect
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity8.141e-056.449e-10InformativeDirect
Molecular Function (MF)hydro-lyase activity0.000773.071e-07InformativeDirect
Molecular Function (MF)racemase and epimerase activity1.214e-052.557e-06InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.52290.05303InformativeInherited
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 activity0.00016570.00161Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.25230.01536Least InformativeInherited
Cellular Component (CC)plastid0.0025167.274e-07InformativeInherited

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 2.164e-11 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 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 1.953e-14 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 4.131e-08 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 1.659e-12 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 1.624e-05 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.736e-13 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 4.668e-11 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 1.439e-05 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 1.94e-05 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) carbohydrate metabolic process 0.002286 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2728 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.199 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.0635 Moderately Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 0 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 1.431e-05 Informative Direct
Biological Process (BP) vitamin metabolic process 0.000221 Informative Direct
Biological Process (BP) carbohydrate catabolic process 4.277e-13 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 1.514e-08 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 7.357e-14 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 3.652e-09 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.0007866 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.0854 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.9769 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0415 Informative Inherited
Biological Process (BP) hexose metabolic process 0.1424 Informative Inherited
Biological Process (BP) pyrimidine nucleotide metabolic process 2.325e-06 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 1.368e-10 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 7.767e-07 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 2.772e-06 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 7.307e-08 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 1.938e-15 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 2.963e-14 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 1.705e-07 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 6.402e-13 Highly Informative Direct
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 3.327e-10 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 6.449e-10 Informative Direct
Molecular Function (MF) hydro-lyase activity 3.071e-07 Informative Direct
Molecular Function (MF) racemase and epimerase activity 2.557e-06 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.05303 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 0.00161 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.01536 Least Informative Inherited
Cellular Component (CC) plastid 7.274e-07 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 synthase9.889e-10Highly 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 functionCobalt2.112e-10InformativeDirect
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 ]