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 (3,207) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 19,200 33,972 45
Proteins 17,632 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 0.00004066 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.4033 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) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.004119 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.000001558 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.001521 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.8181 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.4659 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.109 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4922 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.6203 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.001151 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1078 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.7783 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2782 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.002989 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0.000000004795 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.00000003812 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000004687 Informative Direct
Biological Process (BP) protein catabolic process 0.000004212 Informative Direct
Biological Process (BP) DNA repair 0.00008196 Informative Direct
Biological Process (BP) phosphorylation 0.0005229 Informative Direct
Biological Process (BP) proteolysis 0.001229 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.264 Informative Inherited
Biological Process (BP) nitrogen compound transport 0.001101 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.3285 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.0856 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.01237 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.1516 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.1571 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.2264 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.1497 Informative Inherited
Biological Process (BP) cellular response to external stimulus 0.0334 Informative Inherited
Biological Process (BP) response to nutrient levels 0.1247 Informative Inherited
Biological Process (BP) sexual reproduction 0.1017 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.3416 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 1 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.001696 Informative Inherited
Biological Process (BP) establishment of RNA localization 0.0000000000001378 Highly Informative Direct
Biological Process (BP) regulation of proteolysis involved in cellular protein catabolic process 0.000000000006775 Highly Informative Direct
Biological Process (BP) nuclear export 0.000000000009014 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.00000000004649 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.00000000005025 Highly Informative Direct
Biological Process (BP) macroautophagy 0.00000001976 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.002667 Highly Informative Inherited
Biological Process (BP) negative regulation of transferase activity 0.002239 Highly Informative Inherited
Biological Process (BP) negative regulation of protein phosphorylation 0.006697 Highly Informative Inherited
Molecular Function (MF) binding 0.00001664 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.8885 Least Informative Inherited
Molecular Function (MF) cation binding 0.6357 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.007552 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.01244 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.0007229 Informative Direct
Molecular Function (MF) protein complex binding 0.6643 Informative Inherited
Molecular Function (MF) RNA binding 0.001945 Informative Inherited
Molecular Function (MF) enzyme binding 0.005708 Informative Inherited
Molecular Function (MF) peptidase activity 0.00196 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 0.0000000004844 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.00001242 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.0005019 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.0008749 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.006998 Highly Informative Inherited
Molecular Function (MF) kinase binding 0.02576 Highly Informative Inherited
Molecular Function (MF) structure-specific DNA binding 0.003152 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01704 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2597 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.2415 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000000255 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.01941 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.03969 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.00001348 Informative Direct
Cellular Component (CC) nucleoplasm part 0.2885 Informative Inherited
Cellular Component (CC) integral component of membrane 1 Informative Inherited
Cellular Component (CC) pore complex 0.00001476 Highly Informative Direct
Cellular Component (CC) nuclear body 0.0001845 Highly Informative Direct
Cellular Component (CC) cytoplasmic ribonucleoprotein granule 0.007896 Highly Informative Inherited

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)0.000000005998Least 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 kinases0.0000001025Moderately 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 growth0.1231Least InformativeInherited
Yeast Phenotype (YP)protein/peptide accumulation0.0006513Highly 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)Hydrolases0.00000000004345Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups0.381Least InformativeInherited
Enzyme Commission (EC)Lyases0.8568Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.0000000002483Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.0000003397Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.2903Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.5701Moderately InformativeInherited
Enzyme Commission (EC)Ligases0.7611Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0.00000001859InformativeDirect
Enzyme Commission (EC)Acid--amino-acid ligases (peptide synthases)0.0004086InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processProtein transport0.000000000001457Moderately InformativeDirect
Biological processDifferentiation0.2848Moderately InformativeInherited
Biological processProtein biosynthesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processInflammatory response0.00000006355InformativeDirect
Biological processAutophagy0Highly InformativeDirect
Biological processmRNA transport0.0000000002986Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentLipid droplet0.0000008424Highly InformativeDirect
Cellular componentProteasome0.0001602Highly InformativeDirect
DomainTransit peptide0.000002783Moderately InformativeDirect
DomainLeucine-rich repeat0.0002771InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationProtease0.8584Moderately InformativeInherited
Post-translational modificationThiol protease0.000000002676InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.00001585Least InformativeDirect
Post-translational modificationNitration0.0000296InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism6.774e-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 ]