SUPERFAMILY 1.75 HMM library and genome assignments server

D-ribose-5-phosphate isomerase (RpiA), lid domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   D-ribose-5-phosphate isomerase (RpiA), lid domain [ 75445]
Families:   D-ribose-5-phosphate isomerase (RpiA), lid domain [ 75446]


Superfamily statistics
Genomes (2,193) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,543 13,825 4
Proteins 2,543 13,823 4


Functional annotation
General category Metabolism
Detailed category Carbohydrate metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 0.00000003127 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00000003883 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000007195 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00007162 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00007165 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.05696 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.000000000000005526 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00000000000005029 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.000000003546 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.000000007721 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.00000001245 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0000005061 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000007528 Moderately Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.00000003653 Informative Direct
Biological Process (BP) hexose metabolic process 0.2267 Informative Inherited
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0 Highly Informative Direct
Biological Process (BP) monosaccharide catabolic process 0.00000481 Highly Informative Direct
Biological Process (BP) pentose metabolic process 0.000913 Highly Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 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)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related c0InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)fruit0.00001315InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight 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)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related compounds0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationIsomerase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate degradation0Moderately InformativeDirect
UniPathway (UP)pentose phosphate pathway0Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · 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 4 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 D-ribose-5-phosphate isomerase (RpiA), lid domain 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 4 hidden Markov models representing the D-ribose-5-phosphate isomerase (RpiA), lid domain 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-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]