SUPERFAMILY 1.75 HMM library and genome assignments server


UBA-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   RuvA C-terminal domain-like [ 46928] (9)
Superfamily:   UBA-like [ 46934] (4)
Families:   UBA domain [ 46935] (24)
  TS-N domain [ 63423]
  TAP-C domain-like [ 68973] (2)
  CUE domain [ 88995] (4)


Superfamily statistics
Genomes (3,200) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 18,506 33,972 45
Proteins 17,014 32,445 44


Functional annotation
General category General
Detailed category Protein interaction

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) protein metabolic process 7.93e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.008307 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.4887 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular response to stress 1.577e-06 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0003228 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.7553 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.1526 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.002155 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.6935 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.4412 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.9917 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4689 Moderately Informative Inherited
Biological Process (BP) reproduction 0.8994 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.9196 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.9873 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.001088 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.218 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.0697 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 3.791e-09 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 6.052e-09 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 1.151e-07 Informative Direct
Biological Process (BP) protein catabolic process 8.269e-06 Informative Direct
Biological Process (BP) phosphorylation 0.0002345 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0004171 Informative Direct
Biological Process (BP) nitrogen compound transport 0.0004662 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0005251 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.2653 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.3498 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2848 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.09625 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.1005 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.3111 Informative Inherited
Biological Process (BP) response to nutrient levels 0.09581 Informative Inherited
Biological Process (BP) proteolysis 0.001895 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.08599 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.3853 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 1 Informative Inherited
Biological Process (BP) establishment of RNA localization 1.422e-14 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 6.25e-12 Highly Informative Direct
Biological Process (BP) nuclear export 4.642e-11 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 2.269e-10 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 8.073e-10 Highly Informative Direct
Biological Process (BP) regulation of proteolysis 2.064e-08 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 3.295e-05 Highly Informative Direct
Biological Process (BP) autophagy 0.0002144 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0003482 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.002661 Highly Informative Inherited
Biological Process (BP) cellular response to starvation 0.1906 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.004679 Highly Informative Inherited
Molecular Function (MF) binding 0.0002681 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.9104 Least Informative Inherited
Molecular Function (MF) cation binding 0.6123 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.007017 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.04129 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.000409 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 1 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.186 Informative Inherited
Molecular Function (MF) peptidase activity 0.002111 Informative Inherited
Molecular Function (MF) enzyme binding 0.02806 Informative Inherited
Molecular Function (MF) RNA binding 0.04031 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 6.652e-10 Highly Informative Direct
Molecular Function (MF) manganese ion binding 4.014e-06 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.0008768 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.1089 Highly Informative Inherited
Molecular Function (MF) protein domain specific binding 0.006864 Highly Informative Inherited
Molecular Function (MF) kinase binding 0.004639 Highly Informative Inherited
Molecular Function (MF) structure-specific DNA binding 0.002882 Highly Informative Inherited
Molecular Function (MF) protein binding transcription factor activity 0.001153 Highly Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1178 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1968 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1449 Least Informative Inherited
Cellular Component (CC) nuclear part 1.011e-08 Moderately Informative Direct
Cellular Component (CC) endomembrane system 3.968e-05 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.08528 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.01251 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 1.561e-05 Informative Direct
Cellular Component (CC) integral to membrane 1 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.976 Informative Inherited
Cellular Component (CC) pore complex 1.272e-06 Highly Informative Direct
Cellular Component (CC) nuclear body 2.2e-06 Highly Informative Direct
Cellular Component (CC) proteasome complex 1.919e-05 Highly Informative Direct
Cellular Component (CC) cytoplasmic mRNA processing body 4.75e-05 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)5.998e-09Least InformativeDirect
Enzyme Commission (EC)Ligases0.5691Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.8024Least InformativeInherited
Enzyme Commission (EC)Omega peptidases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases1.025e-07Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.0003685Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds0.02125Moderately InformativeInherited
Enzyme Commission (EC)Acid--D-amino-acid ligases (peptide synthases)0.0001583InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0.1184Least InformativeInherited
Yeast Phenotype (YP)protein/peptide accumulation0.0005651Highly InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases3.939e-11Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups0.3831Least InformativeInherited
Enzyme Commission (EC)Lyases0.8559Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)2.78e-10Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases3.389e-07Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.2915Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.5781Moderately InformativeInherited
Enzyme Commission (EC)Ligases0.7634Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase1.807e-08InformativeDirect
Enzyme Commission (EC)Acid--amino-acid ligases (peptide synthases)0.0004129InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processProtein transport1.504e-12Moderately InformativeDirect
Biological processDifferentiation0.2728Moderately InformativeInherited
Biological processProtein biosynthesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processInflammatory response5.455e-08InformativeDirect
Biological processmRNA transport3.077e-10Highly InformativeDirect
Biological processAutophagy9.98e-05Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentLipid droplet8.516e-07Highly InformativeDirect
Cellular componentProteasome0.0001613Highly InformativeDirect
DomainTransit peptide2.756e-06Moderately InformativeDirect
DomainLeucine-rich repeat0.0002836InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationProtease0.8612Moderately InformativeInherited
Post-translational modificationThiol protease2.695e-09InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationPhosphoprotein1.452e-05Least InformativeDirect
Post-translational modificationNitration2.986e-05InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism8.98e-16Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009060 SSF46934 Protein matches
Abstract

UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases [PubMed12079361]. HHR23A, the human homologue of yeast Rad23A is a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The fold of the UBA domain consists of a compact three-helical bundle with a right-handed twist, and have a conserved hydrophobic surface patch for protein-protein interactions. UBA-like domains can be found in other proteins as well, such as the TS-N domain in the elongation factor Ts (EF-Ts), which catalyses the recycling of the GTPase EF-Tu required for the binding of aminoacyl-tRNA top the ribosomal A site [PubMed11744709]; and the C-terminal domain of TAP/NXF1, which functions in nuclear export through the interaction of its UBA-like domain with FG nucleoporins [PubMed12581645].


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) · Human Phenotype (HP) · 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 39 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 UBA-like 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 39 hidden Markov models representing the UBA-like 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) · Human Phenotype (HP) · 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 ]