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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 (3,205) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 34,512 190,694 41
Proteins 31,321 173,423 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 process0.000045430.000012Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.94951Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.3820.9384Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)response to stimulus0.84741Least InformativeInherited
Biological Process (BP)single-organism cellular process0.38190.222Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.73650.000001848Least InformativeInherited
Biological Process (BP)biosynthetic process0.66110.06413Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.37040.5806Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.6641Least InformativeInherited
Biological Process (BP)peptide metabolic process0.00000024510.000000000000156Moderately InformativeDirect
Biological Process (BP)gene expression0.00000027760.0000000000005623Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000000062320.00000000000004954Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.00020290.000001547Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.000013810.000002193Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.052550.2904Moderately InformativeInherited
Biological Process (BP)response to oxygen-containing compound0.37770.49Moderately InformativeInherited
Biological Process (BP)cellular developmental process0.00064190.8969Moderately InformativeInherited
Biological Process (BP)response to organic substance0.69241Moderately InformativeInherited
Biological Process (BP)system development0.021961Moderately InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.0044270.0000001207Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0016470.0000001791Moderately InformativeInherited
Biological Process (BP)reproduction0.020630.1351Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.000060970.000000000000003764InformativeDirect
Biological Process (BP)central nervous system development0.000000025820.00005258InformativeDirect
Biological Process (BP)pteridine-containing compound metabolic process0.0000013140.000002224InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process0.0000031920.000000000000003764InformativeDirect
Biological Process (BP)carbohydrate derivative catabolic process0.000000014990.00003062InformativeDirect
Biological Process (BP)multicellular organism reproduction0.041990.02171InformativeInherited
Biological Process (BP)cell development0.00013320.07969InformativeInherited
Biological Process (BP)single organism reproductive process0.0049860.05991InformativeInherited
Biological Process (BP)reproductive system development0.017480.001076InformativeInherited
Biological Process (BP)developmental process involved in reproduction0.14250.02201InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.00015160.00612InformativeInherited
Biological Process (BP)amino sugar metabolic process0.0000000000000016070.0000000003185Highly InformativeDirect
Biological Process (BP)translational initiation00Highly InformativeDirect
Biological Process (BP)NADP metabolic process0.00000000067030Highly InformativeDirect
Biological Process (BP)folic acid-containing compound metabolic process0.0000077550.0003179Highly InformativeDirect
Biological Process (BP)sex differentiation0.000023160.00005104Highly InformativeDirect
Biological Process (BP)response to carbohydrate0.00022780.0008277Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.00000021560Highly InformativeDirect
Biological Process (BP)ovulation cycle process0.0000030210.00000000001109Highly InformativeDirect
Biological Process (BP)gliogenesis0.0000000000001950.0000000000005259Highly InformativeDirect
Biological Process (BP)glucose 6-phosphate metabolic process0.000000054180Highly InformativeDirect
Molecular Function (MF)hydrolase activity11Least InformativeInherited
Molecular Function (MF)transferase activity10.8827Least InformativeInherited
Molecular Function (MF)binding0.088790.8813Least InformativeInherited
Molecular Function (MF)isomerase activity0.000000000090980Moderately InformativeDirect
Molecular Function (MF)molecular function regulator0.00000082590.00000000134Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds0.0028820.000006025Moderately InformativeInherited
Molecular Function (MF)anion binding0.011770.1195Moderately InformativeInherited
Molecular Function (MF)small molecule binding0.015540.003737Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000031250.001238Moderately InformativeInherited
Molecular Function (MF)carbohydrate derivative binding0.004680.0258Moderately InformativeInherited
Molecular Function (MF)RNA binding0.00044940.000000008539InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.0000000025170InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity00InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.000031470.0005984InformativeDirect
Molecular Function (MF)ligase activity0.0000010910.002618InformativeInherited
Molecular Function (MF)purine nucleoside binding0.000035390.000001403Highly InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity0.0000000017940.0000000000001448Highly 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 activity00Highly InformativeDirect
Molecular Function (MF)carboxylic ester hydrolase activity0.0000000077360.00000001933Highly InformativeDirect
Cellular Component (CC)macromolecular complex0.033290.02324Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.11010.000000004193Least 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 0.000012 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000001848 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.9384 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) single-organism cellular process 0.222 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.06413 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.5806 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0.000000000000156 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000001207 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000000005623 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000000000004954 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.000001547 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0000001791 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.000002193 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.2904 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.49 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.8969 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2186 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.2694 Moderately Informative Inherited
Biological Process (BP) reproduction 0.1351 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.000000000000003764 Informative Direct
Biological Process (BP) central nervous system development 0.00005258 Informative Direct
Biological Process (BP) pteridine-containing compound metabolic process 0.000002224 Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0.000000000000003764 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.00003062 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.02171 Informative Inherited
Biological Process (BP) cell development 0.07969 Informative Inherited
Biological Process (BP) response to temperature stimulus 0.002171 Informative Inherited
Biological Process (BP) single organism reproductive process 0.05991 Informative Inherited
Biological Process (BP) reproductive system development 0.001076 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.02201 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.00612 Informative Inherited
Biological Process (BP) amino sugar metabolic process 0.0000000003185 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 0.0003179 Highly Informative Direct
Biological Process (BP) sex differentiation 0.00005104 Highly Informative Direct
Biological Process (BP) response to heat 0.00004528 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.0008277 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) ovulation cycle process 0.00000000001109 Highly Informative Direct
Biological Process (BP) gliogenesis 0.0000000000005259 Highly Informative Direct
Biological Process (BP) glucose 6-phosphate metabolic process 0 Highly Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 0.8827 Least Informative Inherited
Molecular Function (MF) binding 0.8813 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.000006025 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.00000000134 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1195 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.003737 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.001238 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.0258 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.000000008539 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) purine ribonucleoside triphosphate binding 0.0005984 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.04471 Informative Inherited
Molecular Function (MF) ligase activity 0.002618 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.003684 Informative Inherited
Molecular Function (MF) purine nucleoside binding 0.000001403 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0000000000001448 Highly Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0 Highly Informative Direct
Molecular Function (MF) thiolester hydrolase activity 0.00009579 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0 Highly Informative Direct
Molecular Function (MF) deaminase activity 0 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.00000001933 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000004193 Least Informative Direct
Cellular Component (CC) macromolecular complex 0.02324 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 system0.0472Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3151Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.4994Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.9149Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.02234Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal genital system morphology0.03678Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.0605Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.1489Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0.2073Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.3Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.3283Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.0000251InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0002086InformativeDirect
Phenotypic Abnormality (PA)Abnormal emotion/affect behavior0.02432InformativeInherited
Phenotypic Abnormality (PA)Gait disturbance0.0594InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.07629InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skull size0.125InformativeInherited
Phenotypic Abnormality (PA)Cognitive impairment0.1832InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the cerebrum0.4382InformativeInherited
Phenotypic Abnormality (PA)Premature ovarian failure0.000003224Highly InformativeDirect
Phenotypic Abnormality (PA)Cerebral hypomyelination0.00001215Highly InformativeDirect
Phenotypic Abnormality (PA)Unsteady gait0.00001338Highly InformativeDirect
Phenotypic Abnormality (PA)Personality changes0.00001472Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.00004478Highly InformativeDirect
Phenotypic Abnormality (PA)Emotional lability0.0001915Highly InformativeDirect
Phenotypic Abnormality (PA)Microcephaly0.06306Highly 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)Hydrolases0.000337Least 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 hydrolases0.000000000003077InformativeDirect
Enzyme Commission (EC)Thiolester hydrolases0.0000235InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Interconverting aldoses and ketoses0Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.00008033Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.3467Highly 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 modificationHydrolase0.0000006248Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationRepressor0.0000007959Moderately InformativeDirect
Post-translational modificationInitiation factor0.000000005604InformativeDirect

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 metabolism0.2765Least 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 biosynthesis9.148e-16Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism1Moderately InformativeInherited
UniPathway (UP)amino-sugar metabolism0InformativeDirect
UniPathway (UP)amine and polyamine degradation0InformativeDirect
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 pathway0.0000004563Highly 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 ]