SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,022) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 13,504 31,438 24
Proteins 13,498 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 3.746e-15 Least Informative Direct
Biological Process (BP) biosynthetic process 4.634e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9162 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.8886 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.545 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.08145 Least Informative Inherited
Biological Process (BP) cellular lipid metabolic process 4.113e-12 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 4.608e-07 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 1.078e-06 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 1.4e-06 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 1.564e-06 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.3951 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1141 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.9605 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.06737 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.004753 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.01467 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.04334 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.1106 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.3487 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.00503 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.01605 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.3131 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4603 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.08487 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.3777 Moderately Informative Inherited
Biological Process (BP) fatty acid metabolic process 1.897e-11 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 1.364e-10 Informative Direct
Biological Process (BP) hexose metabolic process 1.8e-07 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 1.718e-06 Informative Direct
Biological Process (BP) cellular amide metabolic process 5.071e-06 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 5.806e-05 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0008816 Informative Direct
Biological Process (BP) protein complex assembly 0.006198 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.0104 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.2768 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.007681 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.4782 Informative Inherited
Biological Process (BP) monosaccharide biosynthetic process 5.766e-12 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 1.581e-11 Highly Informative Direct
Biological Process (BP) acyl-CoA metabolic process 1.977e-10 Highly Informative Direct
Biological Process (BP) protein tetramerization 1.047e-07 Highly Informative Direct
Biological Process (BP) protein homooligomerization 3.557e-06 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 5.286e-05 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 0.0008735 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.0009528 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.01466 Moderately Informative Inherited
Molecular Function (MF) sulfur compound binding 1.078e-12 Informative Direct
Molecular Function (MF) amide binding 2.075e-11 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 9.601e-10 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 1.94e-08 Informative Direct
Molecular Function (MF) carboxylic acid binding 3.639e-07 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0003292 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0006008 Informative Direct
Molecular Function (MF) nucleotide binding 0.983 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) carboxy-lyase activity 6.512e-12 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 5.643e-11 Highly Informative Direct
Molecular Function (MF) ATP binding 1.401e-10 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 9.847e-11 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.8491 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1145 Least Informative Inherited
Cellular Component (CC) membrane 0.3241 Least Informative Inherited
Cellular Component (CC) mitochondrial part 7.48e-07 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.803e-05 Moderately Informative Direct
Cellular Component (CC) organelle envelope 1.861e-05 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 carboxylase2.558e-15Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylformylglycinamidine cyclo-ligase6.043e-13Highly InformativeDirect
Enzyme Commission (EC)Methylcrotonoyl-CoA carboxylase1.238e-05Highly 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/homeostasis0.154Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0005155Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.003022Moderately InformativeInherited
Phenotypic Abnormality (PA)Hypoglycemia5.645e-05InformativeDirect

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

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 lyases0.05846Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.003928InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0.0181InformativeInherited
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 carboxylase4.009e-05Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases0.5518Highly 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 metabolism0.0003815Moderately InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processLipid biosynthesis8.381e-12InformativeDirect
Biological processFatty acid metabolism1.452e-11InformativeDirect
Biological processGluconeogenesis9.709e-08Highly InformativeDirect
Cellular componentMembrane5.226e-14Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainTransit peptide3.187e-05Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Molecular functionBiotin0Highly InformativeDirect
Molecular functionPyruvate0.0002169Highly InformativeDirect
Post-translational modificationTransferase4.767e-12Least 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)lipid metabolism0Least InformativeDirect
UniPathway (UP)fatty acid metabolism0Moderately InformativeDirect
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0Moderately InformativeDirect
UniPathway (UP)fatty acid biosynthesis0InformativeDirect
UniPathway (UP)malonyl-CoA biosynthesis0Highly 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) · 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]