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 2018_03 genome PDB chains (SCOP 1.75)
Domains 13,836 107,140 24
Proteins 13,826 107,092 24


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

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/homeostasis0.1453Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle tone0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0006642Moderately InformativeDirect
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.0001818InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.004258InformativeInherited
Phenotypic Abnormality (PA)Hypoglycemia0.00008817Highly InformativeDirect

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

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
Xenopus ANatomical entity (XAN)cavitated compound organ0Least 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 lyases0.05919Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0.01416InformativeInherited
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0Highly InformativeDirect
Enzyme Commission (EC)Forming carbon-carbon bonds0Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.00004175Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.582Highly InformativeInherited

Document: EC 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]