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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 (3,072) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,802 79,542 24
Proteins 13,792 79,501 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 0.0000004082 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000009951 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.4809 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.2366 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.1996 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.5756 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8743 Least Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.00000000001437 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0000001857 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000004119 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0000006559 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.000001193 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.00005087 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.0003426 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.103 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.008164 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.4597 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.08954 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.04617 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.02119 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.003733 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.6225 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.654 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.731 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.003376 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.1322 Moderately Informative Inherited
Biological Process (BP) purine-containing compound biosynthetic process 0.00000000000004133 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.00000003452 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00000005169 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.000001006 Informative Direct
Biological Process (BP) protein oligomerization 0.0001314 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.02812 Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.1622 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.5861 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.001545 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0.000000006415 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.00000002003 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000003727 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0.0000003895 Highly Informative Direct
Biological Process (BP) protein homotetramerization 0.0000007707 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.001083 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.000002824 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.00001959 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0001541 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.01569 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0.0000000000001872 Informative Direct
Molecular Function (MF) amide binding 0.0000000001535 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000000002378 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.00000008325 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.0000002412 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0000003152 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.000008366 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.001148 Informative Inherited
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.000000000000205 Highly Informative Direct
Molecular Function (MF) vitamin binding 0.0000000002558 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0000000007107 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0.000000001639 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000001701 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.04817 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0007234 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited

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/homeostasis0.1806Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0005886Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.003751Moderately InformativeInherited
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect
Phenotypic Abnormality (PA)Hypoglycemia0.00007146InformativeDirect
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.0001926InformativeDirect

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 lyases0.06023Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0.01465InformativeInherited
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.00004149Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.5693Highly InformativeInherited
Enzyme Commission (EC)Forming carbon-carbon bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processLipid metabolism0.0002678Moderately InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processLipid biosynthesis0.000000000002168InformativeDirect
Biological processFatty acid metabolism0.000000000003072InformativeDirect
Biological processGluconeogenesis0.0000008881Highly InformativeDirect
Cellular componentMembrane0.0000000000001958Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainTransit peptide0.000003812Moderately InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Molecular functionBiotin0Highly InformativeDirect
Post-translational modificationTransferase0.00000000002577Least 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 metabolism0.00000001041Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.00007046Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0.3217Moderately InformativeInherited
UniPathway (UP)amino-acid degradation0.8509Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0.9638Moderately InformativeInherited
UniPathway (UP)IMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)fatty acid biosynthesis0.0000000000005422InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0.000000001446InformativeDirect
UniPathway (UP)gluconeogenesis0.00000001716InformativeDirect
UniPathway (UP)metabolic intermediate degradation0.003933InformativeInherited
UniPathway (UP)malonyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)L-leucine degradation0.000000000003011Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation0.0000000001179Highly 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) · 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) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]