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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 (3,065) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 13,745 75,026 24
Proteins 13,734 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 0.000000000000003755 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00000005482 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9973 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.7784 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4207 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.04808 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0.0000000001129 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00000008896 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.000001199 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00000146 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.4678 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1475 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.8384 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.06894 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.002466 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.008771 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.0246 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.07247 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.2594 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.005205 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.016 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4563 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.6161 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.05335 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.3707 Moderately Informative Inherited
Biological Process (BP) purine-containing compound biosynthetic process 0.00000000002047 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.00000000002395 Informative Direct
Biological Process (BP) hexose metabolic process 0.0000002378 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.000002549 Informative Direct
Biological Process (BP) protein oligomerization 0.00006076 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.00007233 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0001393 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.009517 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 1 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.2527 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.00788 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.3376 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.4523 Informative Inherited
Biological Process (BP) monosaccharide biosynthetic process 0.000000000008813 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.00000000002299 Highly Informative Direct
Biological Process (BP) acyl-CoA metabolic process 0.0000000001746 Highly Informative Direct
Biological Process (BP) protein tetramerization 0.0000001678 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.000005284 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.00005253 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 0.0007679 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.000511 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.01871 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0.00000000000007162 Informative Direct
Molecular Function (MF) amide binding 0.000000000002499 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.000000001769 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.00000004189 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.00000006075 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0004424 Informative Direct
Molecular Function (MF) nucleotide binding 1 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.001987 Informative Inherited
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.00000000001062 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0.00000000006739 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0000000003376 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000000007908 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01796 Least Informative Inherited
Cellular Component (CC) membrane 0.3537 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0000006984 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.0000386 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.00006095 Moderately 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 metabolism/homeostasis0.1507Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.000514Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.002898Moderately InformativeInherited
Phenotypic Abnormality (PA)Hypoglycemia0.00005628InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0Least InformativeDirect

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

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)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least 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 lyases0.05933Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.004137InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0.01694InformativeInherited
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 carboxylase0.00003996Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.5378Highly InformativeInherited
Enzyme Commission (EC)Ligases that form 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 metabolism0.0003928Moderately InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processLipid biosynthesis0.000000000008214InformativeDirect
Biological processFatty acid metabolism0.00000000001147InformativeDirect
Biological processGluconeogenesis0.00000009263Highly InformativeDirect
Cellular componentMembrane0.00000000000005541Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainTransit peptide0.00003544Moderately 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 functionPyruvate0.0002083Highly InformativeDirect
Post-translational modificationTransferase0.000000000004108Least 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 metabolism0.00000001958Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.00006227Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0.3816Moderately InformativeInherited
UniPathway (UP)amino-acid degradation0.8498Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)IMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)fatty acid biosynthesis0.000000000001242InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0.000000001639InformativeDirect
UniPathway (UP)gluconeogenesis0.00000001472InformativeDirect
UniPathway (UP)metabolic intermediate degradation0.01447InformativeInherited
UniPathway (UP)malonyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)L-leucine degradation0.000000000003059Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation0.000000003621Highly 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) · Mouse Phenotype (MP) · 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) · Mouse Phenotype (MP) · 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 ]