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 (2,362)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	10,906	31,438	24
Proteins	10,901	31,428	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	2.154e-07	Least Informative	Direct
Biological Process (BP)	cellular aromatic compound metabolic process	1	Least Informative	Inherited
Biological Process (BP)	organic cyclic compound metabolic process	1	Least Informative	Inherited
Biological Process (BP)	cellular component organization or biogenesis	0.9465	Least Informative	Inherited
Biological Process (BP)	heterocycle metabolic process	0.9195	Least Informative	Inherited
Biological Process (BP)	nitrogen compound metabolic process	0.4454	Least Informative	Inherited
Biological Process (BP)	cellular lipid metabolic process	1.131e-11	Moderately Informative	Direct
Biological Process (BP)	cofactor metabolic process	1.069e-06	Moderately Informative	Direct
Biological Process (BP)	monocarboxylic acid metabolic process	3.807e-06	Moderately Informative	Direct
Biological Process (BP)	lipid biosynthetic process	9.061e-06	Moderately Informative	Direct
Biological Process (BP)	cellular component biogenesis	0.3583	Moderately Informative	Inherited
Biological Process (BP)	macromolecular complex subunit organization	0.1123	Moderately Informative	Inherited
Biological Process (BP)	small molecule biosynthetic process	0.04811	Moderately Informative	Inherited
Biological Process (BP)	organophosphate metabolic process	0.01108	Moderately Informative	Inherited
Biological Process (BP)	phosphate-containing compound metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	nucleobase-containing small molecule metabolic process	0.004857	Moderately Informative	Inherited
Biological Process (BP)	aromatic compound biosynthetic process	0.01125	Moderately Informative	Inherited
Biological Process (BP)	cellular nitrogen compound biosynthetic process	0.01788	Moderately Informative	Inherited
Biological Process (BP)	heterocycle biosynthetic process	0.02554	Moderately Informative	Inherited
Biological Process (BP)	organic cyclic compound biosynthetic process	0.1552	Moderately Informative	Inherited
Biological Process (BP)	cellular amino acid metabolic process	0.0104	Moderately Informative	Inherited
Biological Process (BP)	cellular catabolic process	0.277	Moderately Informative	Inherited
Biological Process (BP)	organic substance catabolic process	0.5706	Moderately Informative	Inherited
Biological Process (BP)	organonitrogen compound biosynthetic process	0.2627	Moderately Informative	Inherited
Biological Process (BP)	carbohydrate metabolic process	0.6173	Moderately Informative	Inherited
Biological Process (BP)	fatty acid metabolic process	2.872e-11	Informative	Direct
Biological Process (BP)	purine-containing compound biosynthetic process	1.718e-10	Informative	Direct
Biological Process (BP)	monocarboxylic acid biosynthetic process	4.503e-06	Informative	Direct
Biological Process (BP)	protein oligomerization	5.958e-05	Informative	Direct
Biological Process (BP)	hexose metabolic process	0.0001095	Informative	Direct
Biological Process (BP)	nucleotide biosynthetic process	0.0004965	Informative	Direct
Biological Process (BP)	carbohydrate biosynthetic process	0.122	Informative	Inherited
Biological Process (BP)	carboxylic acid catabolic process	0.005148	Informative	Inherited
Biological Process (BP)	organonitrogen compound catabolic process	0.04481	Informative	Inherited
Biological Process (BP)	purine nucleotide metabolic process	0.1503	Informative	Inherited
Biological Process (BP)	acyl-CoA metabolic process	7.384e-10	Highly Informative	Direct
Biological Process (BP)	nucleobase metabolic process	1.233e-08	Highly Informative	Direct
Biological Process (BP)	monosaccharide biosynthetic process	1.165e-07	Highly Informative	Direct
Biological Process (BP)	protein tetramerization	1.714e-07	Highly Informative	Direct
Biological Process (BP)	protein homooligomerization	6.088e-06	Highly Informative	Direct
Biological Process (BP)	nucleoside monophosphate metabolic process	3.474e-05	Highly Informative	Direct
Biological Process (BP)	branched-chain amino acid metabolic process	6.761e-05	Highly Informative	Direct
Molecular Function (MF)	binding	1	Least Informative	Inherited
Molecular Function (MF)	heterocyclic compound binding	0.03657	Moderately Informative	Inherited
Molecular Function (MF)	organic cyclic compound binding	0.04171	Moderately Informative	Inherited
Molecular Function (MF)	anion binding	0.001044	Moderately Informative	Inherited
Molecular Function (MF)	lyase activity	0.06102	Moderately Informative	Inherited
Molecular Function (MF)	carboxylic acid binding	1.418e-08	Informative	Direct
Molecular Function (MF)	carbon-carbon lyase activity	3.348e-07	Informative	Direct
Molecular Function (MF)	nucleotide binding	1	Informative	Inherited
Molecular Function (MF)	ligase activity, forming carbon-nitrogen bonds	1	Informative	Inherited
Molecular Function (MF)	monocarboxylic acid binding	0	Highly Informative	Direct
Molecular Function (MF)	sulfur compound binding	2.744e-14	Highly Informative	Direct
Molecular Function (MF)	carboxy-lyase activity	7.541e-09	Highly Informative	Direct
Molecular Function (MF)	ATP binding	8.796e-09	Highly Informative	Direct
Cellular Component (CC)	cytoplasmic part	7.786e-10	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	1	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.05154	Least Informative	Inherited
Cellular Component (CC)	membrane	0.2767	Least Informative	Inherited
Cellular Component (CC)	mitochondrial part	1.16e-06	Moderately Informative	Direct
Cellular Component (CC)	organelle membrane	2.012e-05	Moderately Informative	Direct
Cellular Component (CC)	organelle envelope	3.959e-05	Moderately Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Ligases	0	Least Informative	Direct
Enzyme Commission (EC)	Lyases	1	Least Informative	Inherited
Enzyme Commission (EC)	Transferring one-carbon groups	1	Least Informative	Inherited
Enzyme Commission (EC)	Forming carbon-nitrogen bonds	0	Moderately Informative	Direct
Enzyme Commission (EC)	Carboxy-lyases	0.004926	Moderately Informative	Inherited
Enzyme Commission (EC)	Other carbon--nitrogen ligases	0	Informative	Direct
Enzyme Commission (EC)	Ligases that form carbon-carbon bonds	1	Informative	Inherited
Enzyme Commission (EC)	Cyclo-ligases	0.7611	Informative	Inherited
Enzyme Commission (EC)	Hydroxymethyl-, formyl- and related transferases	0.02166	Informative	Inherited
Enzyme Commission (EC)	Biotin carboxylase	0	Highly Informative	Direct
Enzyme Commission (EC)	Phosphoribosylaminoimidazole carboxylase	0	Highly Informative	Direct
Enzyme Commission (EC)	Phosphoribosylglycinamide formyltransferase	0	Highly Informative	Direct
Enzyme Commission (EC)	5-(carboxyamino)imidazole ribonucleotide synthase	0	Highly Informative	Direct
Enzyme Commission (EC)	Phosphoribosylamine--glycine ligase	0	Highly Informative	Direct
Enzyme Commission (EC)	Pyruvate carboxylase	2.558e-15	Highly Informative	Direct
Enzyme Commission (EC)	Phosphoribosylformylglycinamidine cyclo-ligase	6.043e-13	Highly Informative	Direct
Enzyme Commission (EC)	Methylcrotonoyl-CoA carboxylase	1.238e-05	Highly Informative	Direct

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)

	DO term	FDR (all)	SDDO level	Annotation (direct or inherited)
Disease Ontology (DO)	disease of metabolism	0	Moderately Informative	Direct
Disease Ontology (DO)	glucose metabolism disease	1	Informative	Inherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)

	HP term	FDR (all)	SDHP level	Annotation (direct or inherited)
Phenotypic Abnormality (PA)	Abnormality of metabolism/homeostasis	0.1485	Least Informative	Inherited
Phenotypic Abnormality (PA)	Abnormality of acid-base homeostasis	0.0004609	Moderately Informative	Direct
Phenotypic Abnormality (PA)	Hypoglycemia	5.039e-05	Informative	Direct
Phenotypic Abnormality (PA)	Acidosis	0.0003425	Informative	Direct

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)

	MP term	FDR (all)	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	abnormal homeostasis	0	Least Informative	Direct

Document: MP 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 term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	male genitalia	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	head	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	viscus	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	portion of tissue	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	gonad	0	Least Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	shoot apex	0	Least Informative	Direct
Plant ANatomical entity (PAN)	root	0	Least Informative	Direct
Plant ANatomical entity (PAN)	plant embryo	0	Least Informative	Direct
Plant ANatomical entity (PAN)	seed	0	Least Informative	Direct
Plant ANatomical entity (PAN)	vascular leaf	0	Least Informative	Direct
Plant ANatomical entity (PAN)	megasporophyll	0	Least Informative	Direct
Plant ANatomical entity (PAN)	sepal	0	Least Informative	Direct
Plant ANatomical entity (PAN)	petal	0	Least Informative	Direct
Plant ANatomical entity (PAN)	pedicel	0	Least Informative	Direct
Plant ANatomical entity (PAN)	gynoecium	0	Least Informative	Direct
Plant ANatomical entity (PAN)	collective leaf structure	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	C globular stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Lyases	1	Least Informative	Inherited
Enzyme Commission (EC)	Ligases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Carbon-carbon lyases	0.05988	Moderately Informative	Inherited
Enzyme Commission (EC)	Transferring one-carbon groups	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Other carbon--nitrogen ligases	0	Informative	Direct
Enzyme Commission (EC)	Carboxy-lyases	0.004233	Informative	Inherited
Enzyme Commission (EC)	Hydroxymethyl-, formyl- and related transferases	0.01947	Informative	Inherited
Enzyme Commission (EC)	Phosphoribosylglycinamide formyltransferase	0	Highly Informative	Direct
Enzyme Commission (EC)	Phosphoribosylaminoimidazole carboxylase	0	Highly Informative	Direct
Enzyme Commission (EC)	Phosphoribosylamine--glycine ligase	0	Highly Informative	Direct
Enzyme Commission (EC)	Biotin carboxylase	0	Highly Informative	Direct
Enzyme Commission (EC)	Urea carboxylase	4.892e-05	Highly Informative	Direct
Enzyme Commission (EC)	Cyclo-ligases	0.6778	Highly Informative	Inherited
Enzyme Commission (EC)	Ligases that form carbon-carbon bonds	1	Highly Informative	Inherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)

	DB term	FDR (all)	SDDB level	Annotation (direct or inherited)
Drugbank ATC_code (DB)	vitamins	0	Least Informative	Direct
Drugbank ATC_code (DB)	other plain vitamin preparations	1	Moderately Informative	Inherited

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Transport	0	Least Informative	Direct
Biological process	Lipid metabolism	0.0003574	Moderately Informative	Direct
Biological process	Electron transport	0	Informative	Direct
Biological process	Photosynthesis	0	Informative	Direct
Biological process	Purine biosynthesis	0	Informative	Direct
Biological process	Lipid biosynthesis	8.005e-12	Informative	Direct
Biological process	Fatty acid metabolism	1.748e-11	Informative	Direct
Biological process	Gluconeogenesis	1.081e-07	Highly Informative	Direct
Cellular component	Membrane	3.299e-14	Least Informative	Direct
Cellular component	Plastid	0	Moderately Informative	Direct
Cellular component	Thylakoid	0	Informative	Direct
Domain	Signal	0	Least Informative	Direct
Domain	Transmembrane	0	Least Informative	Direct
Domain	Transit peptide	6.485e-05	Moderately Informative	Direct
Molecular function	Metal-binding	0	Least Informative	Direct
Molecular function	Nucleotide-binding	0	Least Informative	Direct
Molecular function	Iron	0	Moderately Informative	Direct
Molecular function	Magnesium	0	Moderately Informative	Direct
Molecular function	Manganese	0	Moderately Informative	Direct
Molecular function	Heme	0	Informative	Direct
Molecular function	Biotin	0	Highly Informative	Direct
Molecular function	Pyruvate	7.875e-06	Highly Informative	Direct
Post-translational modification	Transferase	1.601e-12	Least Informative	Direct
Post-translational modification	Ligase	0	Moderately Informative	Direct

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)

	UP term	FDR (all)	SDUP level	Annotation (direct or inherited)
UniPathway (UP)	aromatic compound metabolism	0	Least Informative	Direct
UniPathway (UP)	amino-acid metabolism	1	Least Informative	Inherited
UniPathway (UP)	carbohydrate metabolism	1	Least Informative	Inherited
UniPathway (UP)	lipid metabolism	1	Least Informative	Inherited
UniPathway (UP)	nucleotide metabolism	0	Moderately Informative	Direct
UniPathway (UP)	purine metabolism	0	Moderately Informative	Direct
UniPathway (UP)	fatty acid metabolism	2.297e-08	Moderately Informative	Direct
UniPathway (UP)	carbohydrate biosynthesis	6.541e-05	Moderately Informative	Direct
UniPathway (UP)	lipid biosynthesis	0.371	Moderately Informative	Inherited
UniPathway (UP)	amino-acid degradation	0.848	Moderately Informative	Inherited
UniPathway (UP)	metabolic intermediate biosynthesis	1	Moderately Informative	Inherited
UniPathway (UP)	IMP biosynthesis via de novo pathway	0	Informative	Direct
UniPathway (UP)	fatty acid biosynthesis	7.94e-13	Informative	Direct
UniPathway (UP)	Branched-chain amino-acid degradation	1.74e-09	Informative	Direct
UniPathway (UP)	gluconeogenesis	1.503e-08	Informative	Direct
UniPathway (UP)	metabolic intermediate degradation	0.01474	Informative	Inherited
UniPathway (UP)	malonyl-CoA biosynthesis	0	Highly Informative	Direct
UniPathway (UP)	L-leucine degradation	3.254e-12	Highly Informative	Direct
UniPathway (UP)	propanoyl-CoA degradation	3.038e-09	Highly Informative	Direct

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 [ PubMed 10423236], as well as in the C-terminal domain of the biotin carboxylase subunit of acetyl-CoA carboxylase [ PubMed 10821865], and its family members, such as glycinamide ribonucleotide synthetase C-terminal domain [ PubMed 9843369], N5-carboxyaminoimidazole ribonucleotide synthetase PurK C-terminal domain [ PubMed 10569930], and glycinamide ribonucleotide transformylase PurT C-terminal domain [ PubMed 11953435].

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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.

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Rudiment single hybrid motif superfamily