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Rudiment single hybrid motif superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Barrel-sandwich hybrid [ 51229] (4)
Superfamily:   Rudiment single hybrid motif [ 51246] (2)
Families:   BC C-terminal domain-like [ 51247] (5)
  Cytochrome f, small domain [ 51256]


Superfamily statistics
Genomes (3,067) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 13,772 75,026 24
Proteins 13,762 75,012 24


Functional annotation
General category Processes_IC
Detailed category 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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0000004358 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000007658 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0001154 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.5077 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.4834 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1737 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.7857 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.1041 Least Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.00000000000005973 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.00000000005605 Moderately Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0.0000000007727 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0000005989 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000007341 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound biosynthetic process 0.00000184 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.000002734 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00000645 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.0000376 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.000653 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.1896 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1893 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.1357 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative biosynthetic process 0.05798 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.478 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.5101 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.7148 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.003678 Moderately Informative Inherited
Biological Process (BP) purine-containing compound biosynthetic process 0.0000000000000208 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00000006063 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0000001609 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.000005218 Informative Direct
Biological Process (BP) protein oligomerization 0.00004449 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.02389 Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.1583 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.4401 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.02604 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.001847 Informative Inherited
Biological Process (BP) glucose metabolic process 0.00000001064 Highly Informative Direct
Biological Process (BP) protein homotetramerization 0.0000002177 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.000000282 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000004413 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0.00000332 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.0006913 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.0000005507 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.000009222 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0004018 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.01195 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0.000000000001433 Informative Direct
Molecular Function (MF) amide binding 0.00000000006323 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000000001244 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.000000003584 Informative Direct
Molecular Function (MF) ribonucleoside binding 0.00000004527 Informative Direct
Molecular Function (MF) purine nucleoside binding 0.00000004666 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.0000001063 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0000001381 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00004126 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0001491 Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0.00000000000009573 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.0000000000001227 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0000000003002 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000003484 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1041 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0005182 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.9867 Moderately Informative Inherited
Cellular Component (CC) lipid particle 0.00002338 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Forming carbon-nitrogen bonds0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.004926Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0InformativeDirect
Enzyme Commission (EC)Ligases that form carbon-carbon bonds1InformativeInherited
Enzyme Commission (EC)Cyclo-ligases0.7611InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0.02166InformativeInherited
Enzyme Commission (EC)Biotin carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylaminoimidazole carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0Highly InformativeDirect
Enzyme Commission (EC)5-(carboxyamino)imidazole ribonucleotide synthase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0Highly InformativeDirect
Enzyme Commission (EC)Pyruvate carboxylase0.000000000000002558Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylformylglycinamidine cyclo-ligase0.0000000000006043Highly InformativeDirect
Enzyme Commission (EC)Methylcrotonoyl-CoA carboxylase0.00001238Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)disease of metabolism0Moderately InformativeDirect
Disease Ontology (DO)glucose metabolism disease1InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the musculature0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.182Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0005784Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.003752Moderately InformativeInherited
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect
Phenotypic Abnormality (PA)Hypoglycemia0.00007145InformativeDirect
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.0001988InformativeDirect
Phenotypic Abnormality (PA)Acidosis0.0004446InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP 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)head0Least InformativeDirect

Document: XA 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)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.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)Lyases1Least InformativeInherited
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0.06238Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0.01512InformativeInherited
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylaminoimidazole carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0Highly InformativeDirect
Enzyme Commission (EC)Biotin carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.0000406Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.5604Highly InformativeInherited
Enzyme Commission (EC)Forming carbon-carbon bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)alimentary tract and metabolism0.001998Least InformativeInherited
Drugbank ATC_code (DB)other plain vitamin preparations1Moderately InformativeInherited
Drugbank ATC_code (DB)biotin0.0000000000004284InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processLipid metabolism0.000278Moderately InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processLipid biosynthesis0.00000000000216InformativeDirect
Biological processFatty acid metabolism0.00000000000326InformativeDirect
Biological processGluconeogenesis0.0000009408Highly InformativeDirect
Cellular componentMembrane0.0000000000001344Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainTransit peptide0.000008145Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Molecular functionBiotin0Highly InformativeDirect
Molecular functionPyruvate0.0001898Highly InformativeDirect
Post-translational modificationTransferase0.000000000006869Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)nucleotide metabolism0Moderately InformativeDirect
UniPathway (UP)purine metabolism0Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism0.00000001034Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.00007037Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0.3195Moderately InformativeInherited
UniPathway (UP)amino-acid degradation0.8499Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0.9628Moderately InformativeInherited
UniPathway (UP)IMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)fatty acid biosynthesis0.0000000000005452InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0.000000001607InformativeDirect
UniPathway (UP)gluconeogenesis0.00000001711InformativeDirect
UniPathway (UP)metabolic intermediate degradation0.0149InformativeInherited
UniPathway (UP)malonyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)L-leucine degradation0.000000000003Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation0.000000004427Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011054 SSF51246 Protein matches
Abstract

The rudiment single hybrid motif has a beta-barrel sandwich hybrid motif, consisting of a sandwich of half-barrel shaped beta-sheets. This motif is found in the small domain of cytochrome f [PubMed10423236], as well as in the C-terminal domain of the biotin carboxylase subunit of acetyl-CoA carboxylase [PubMed10821865], and its family members, such as glycinamide ribonucleotide synthetase C-terminal domain [PubMed9843369], N5-carboxyaminoimidazole ribonucleotide synthetase PurK C-terminal domain [PubMed10569930], and glycinamide ribonucleotide transformylase PurT C-terminal domain [PubMed11953435].


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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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 12 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 Rudiment single hybrid motif 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 12 hidden Markov models representing the Rudiment single hybrid motif 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]