SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (3,074) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,836 79,542 24
Proteins 13,826 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 0.000001071 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000359 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.6354 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.4393 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.9047 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.2759 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.4769 Least Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.00000000006677 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00000001596 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.00000004846 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.000001009 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000001088 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.000061 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.000586 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.001633 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1184 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.5422 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.01121 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.07104 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.01184 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.6791 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.004672 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.5172 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6024 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.06797 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.1632 Moderately Informative Inherited
Biological Process (BP) purine-containing compound biosynthetic process 0.000000000000003734 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.00000003298 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00000004449 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.0000009203 Informative Direct
Biological Process (BP) protein oligomerization 0.0001919 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.001495 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.5773 Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.1777 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.03201 Informative Inherited
Biological Process (BP) hexose biosynthetic process 0.0000000002323 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.0000000005014 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000000233 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000003619 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0.0000004778 Highly Informative Direct
Biological Process (BP) protein homotetramerization 0.0000009042 Highly Informative Direct
Biological Process (BP) pigmentation 0.0003456 Highly Informative Direct
Biological Process (BP) response to drug 0.0009206 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 0.000000208 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0000006169 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00004776 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.02022 Moderately Informative Inherited
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) amide binding 0.000000000001912 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000000003393 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.000000002261 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.000000006285 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.000000008656 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00001126 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0002011 Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.0000000000003087 Highly Informative Direct
Molecular Function (MF) vitamin binding 0.000000000003929 Highly Informative Direct
Molecular Function (MF) ATP binding 0.000000000006668 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0.000000001755 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000002755 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05332 Least Informative Inherited
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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processLipid metabolism0.0002707Moderately InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processLipid biosynthesis0.00000000000203InformativeDirect
Biological processFatty acid metabolism0.00000000000285InformativeDirect
Biological processGluconeogenesis0.0000008524Highly InformativeDirect
Cellular componentMembrane0.000000000000279Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransit peptide0.000003907Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Molecular functionBiotin0Highly InformativeDirect
Post-translational modificationTransferase0.00000000002321Least InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]