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NagB/RpiA/CoA transferase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   NagB/RpiA/CoA transferase-like [ 100949]
Superfamily:   NagB/RpiA/CoA transferase-like [ 100950] (8)
Families:   NagB-like [ 52513] (2)
  D-ribose-5-phosphate isomerase (RpiA), catalytic domain [ 75176]
  CoA transferase beta subunit-like [ 74657] (3)
  CoA transferase alpha subunit-like [ 74656] (6)
  IF2B-like [ 110513] (5)
  Methenyltetrahydrofolate synthetase [ 110520] (3)
  YkgG-like [ 142200]
  SorC sugar-binding domain-like [ 159545] (5)


Superfamily statistics
Genomes (3,200) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 34,410 219,592 41
Proteins 31,234 196,804 34


Functional annotation
General category Metabolism
Detailed category Transferases

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 nitrogen compound metabolic process0.00018160.00007873Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.00088510.0000000001937Least InformativeDirect
Biological Process (BP)single-organism cellular process0.66650.4555Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.76441Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.95851Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.60530.05356Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.74430.00000137Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)response to stimulus0.87491Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.48161Least InformativeInherited
Biological Process (BP)peptide metabolic process0.000027280.000007779Moderately InformativeDirect
Biological Process (BP)gene expression0.00000022650.0000000000006264Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000000066620.00000000000006612Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.00018450.000000805Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.072810.2263Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0040850.0000004166Moderately InformativeInherited
Biological Process (BP)cellular developmental process0.000590.3815Moderately InformativeInherited
Biological Process (BP)response to organic substance0.67161Moderately InformativeInherited
Biological Process (BP)response to oxygen-containing compound0.3730.4659Moderately InformativeInherited
Biological Process (BP)system development0.023471Moderately InformativeInherited
Biological Process (BP)reproduction0.019770.134Moderately InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.014540.0000004892Moderately InformativeInherited
Biological Process (BP)ribose phosphate metabolic process0.12940.00001895Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.00022740.0000000000000208InformativeDirect
Biological Process (BP)central nervous system development0.000000026160.00004947InformativeDirect
Biological Process (BP)pteridine-containing compound metabolic process0.0000080420.00002973InformativeDirect
Biological Process (BP)carbohydrate derivative catabolic process0.000000049190.0001144InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.18580.01608InformativeInherited
Biological Process (BP)multicellular organism reproduction0.032430.01822InformativeInherited
Biological Process (BP)single organism reproductive process0.0035430.05833InformativeInherited
Biological Process (BP)cell development0.00011880.07292InformativeInherited
Biological Process (BP)developmental process involved in reproduction0.13510.02177InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.00015830.007106InformativeInherited
Biological Process (BP)pyridine-containing compound metabolic process0.0055180.00000001275InformativeInherited
Biological Process (BP)reproductive system development0.01690.0009888InformativeInherited
Biological Process (BP)amino sugar metabolic process0.0000000000000087830.000000001978Highly InformativeDirect
Biological Process (BP)translational initiation00Highly InformativeDirect
Biological Process (BP)NADP metabolic process0.000000011880Highly InformativeDirect
Biological Process (BP)folic acid-containing compound metabolic process0.0000070640.0003407Highly InformativeDirect
Biological Process (BP)sex differentiation0.000019940.00004416Highly InformativeDirect
Biological Process (BP)response to carbohydrate0.00023070.0007593Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.0000011840Highly InformativeDirect
Biological Process (BP)ovulation cycle process0.0000034080.000000000007716Highly InformativeDirect
Biological Process (BP)gliogenesis0.00000000000019920.000000000003587Highly InformativeDirect
Biological Process (BP)glucose 6-phosphate metabolic process0.00000023370Highly InformativeDirect
Molecular Function (MF)hydrolase activity11Least InformativeInherited
Molecular Function (MF)transferase activity10.7818Least InformativeInherited
Molecular Function (MF)binding0.061960.8345Least InformativeInherited
Molecular Function (MF)isomerase activity0.00000000070760Moderately InformativeDirect
Molecular Function (MF)molecular function regulator0.00000053780.0000000005907Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds0.0028560.0000219Moderately InformativeInherited
Molecular Function (MF)anion binding0.0099080.1014Moderately InformativeInherited
Molecular Function (MF)carbohydrate derivative binding0.0039610.02282Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000011950.001134Moderately InformativeInherited
Molecular Function (MF)small molecule binding0.0066630.00192Moderately InformativeInherited
Molecular Function (MF)purine nucleoside binding0.000063840.0008635InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.0000000026280InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity00InformativeDirect
Molecular Function (MF)ribonucleoside binding0.000058840.0008461InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.000025690.0005193InformativeDirect
Molecular Function (MF)ligase activity0.00000092360.002225InformativeInherited
Molecular Function (MF)RNA binding0.0012450.000000002003InformativeInherited
Molecular Function (MF)guanyl-nucleotide exchange factor activity0.0000000011860.0000000000001177Highly InformativeDirect
Molecular Function (MF)translation factor activity, RNA binding00Highly InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity, interconverting aldoses and ketoses00Highly InformativeDirect
Molecular Function (MF)deaminase activity00.000000000000003237Highly InformativeDirect
Molecular Function (MF)carboxylic ester hydrolase activity0.0000000076260.000000005044Highly InformativeDirect
Cellular Component (CC)protein complex0.00027930.00002184Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.071340.00000000008918Least InformativeInherited

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 nitrogen compound metabolic process 0.00007873 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00000137 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000000001937 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.4555 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.05356 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0.000007779 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000004892 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000000006264 Moderately Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0.00001895 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000000000006612 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.000000805 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0000004166 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.7748 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.3815 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.4659 Moderately Informative Inherited
Biological Process (BP) response to stress 0.9698 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2964 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.134 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2263 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.0000000000000208 Informative Direct
Biological Process (BP) central nervous system development 0.00004947 Informative Direct
Biological Process (BP) pteridine-containing compound metabolic process 0.00002973 Informative Direct
Biological Process (BP) reproductive system development 0.0009888 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.00000001275 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.0001144 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.01608 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.01822 Informative Inherited
Biological Process (BP) single organism reproductive process 0.05833 Informative Inherited
Biological Process (BP) cell development 0.07292 Informative Inherited
Biological Process (BP) response to temperature stimulus 0.001934 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.02177 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.007106 Informative Inherited
Biological Process (BP) amino sugar metabolic process 0.000000001978 Highly Informative Direct
Biological Process (BP) translational initiation 0 Highly Informative Direct
Biological Process (BP) NADP metabolic process 0 Highly Informative Direct
Biological Process (BP) folic acid-containing compound metabolic process 0.0003407 Highly Informative Direct
Biological Process (BP) sex differentiation 0.00004416 Highly Informative Direct
Biological Process (BP) response to heat 0.00004044 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.0007593 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) ovulation cycle process 0.000000000007716 Highly Informative Direct
Biological Process (BP) gliogenesis 0.000000000003587 Highly Informative Direct
Biological Process (BP) glucose 6-phosphate metabolic process 0 Highly Informative Direct
Molecular Function (MF) binding 0.8345 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 0.7818 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.0000219 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.0000000005907 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.02282 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.00192 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.001134 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.1014 Moderately Informative Inherited
Molecular Function (MF) purine nucleoside binding 0.0008635 Informative Direct
Molecular Function (MF) RNA binding 0.000000002003 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0 Informative Direct
Molecular Function (MF) ribonucleoside binding 0.0008461 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0005193 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.04835 Informative Inherited
Molecular Function (MF) ligase activity 0.002225 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.003865 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0000000000001177 Highly Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0 Highly Informative Direct
Molecular Function (MF) deaminase activity 0.000000000000003237 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.000000005044 Highly Informative Direct
Cellular Component (CC) protein complex 0.00002184 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000008918 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited

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)Ligases1Least InformativeInherited
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Carboxylic ester hydrolases0.00000000000001442Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related c0InformativeDirect
Enzyme Commission (EC)Thiolester hydrolases0.00002533InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.01457InformativeInherited
Enzyme Commission (EC)In other compounds0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Juvenile onset0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.04697Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3108Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.5333Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.9139Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.02228Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal genital system morphology0.03606Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.05906Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.1509Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0.2058Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.2986Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.326Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.00002431InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0002059InformativeDirect
Phenotypic Abnormality (PA)Abnormal emotion/affect behavior0.02356InformativeInherited
Phenotypic Abnormality (PA)Gait disturbance0.05863InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.07763InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skull size0.1227InformativeInherited
Phenotypic Abnormality (PA)Cognitive impairment0.184InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the cerebrum0.4388InformativeInherited
Phenotypic Abnormality (PA)Premature ovarian failure0.000003339Highly InformativeDirect
Phenotypic Abnormality (PA)Cerebral hypomyelination0.00001252Highly InformativeDirect
Phenotypic Abnormality (PA)Personality changes0.00001522Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.00004627Highly InformativeDirect
Phenotypic Abnormality (PA)Emotional lability0.0001809Highly InformativeDirect
Phenotypic Abnormality (PA)Microcephaly0.06176Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
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)Hydrolases0.0004123Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-OH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Carboxylic ester hydrolases0.000000000004039InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Cyclo-ligases0.00008736Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.3538Highly 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 processMethionine biosynthesis0Highly InformativeDirect
Post-translational modificationHydrolase0.00001146Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationRepressor0.000004561Moderately InformativeDirect
Post-translational modificationInitiation factor0.00000001377InformativeDirect

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)amino-acid metabolism0.2637Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate degradation0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis4.579e-16Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism1Moderately InformativeInherited
UniPathway (UP)amino-sugar metabolism0InformativeDirect
UniPathway (UP)amine and polyamine degradation0InformativeDirect
UniPathway (UP)L-methionine biosynthesis0InformativeDirect
UniPathway (UP)pentose phosphate pathway0Highly InformativeDirect
UniPathway (UP)N-acetylneuraminate degradation0Highly InformativeDirect
UniPathway (UP)L-methionine biosynthesis via salvage pathway0Highly InformativeDirect
UniPathway (UP)beta-ketoadipate pathway0.0000004579Highly InformativeDirect
UniPathway (UP)ketone degradation1Highly InformativeInherited

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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 32 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 NagB/RpiA/CoA transferase-like 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 32 hidden Markov models representing the NagB/RpiA/CoA transferase-like 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]