SUPERFAMILY 1.75 HMM library and genome assignments server

Please note: Superfamily is currently under maintenance and some functionality may be limited. Please bear with us as we fix these problems.


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 (3,206) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 19,120 33,972 45
Proteins 17,559 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 0.00002224 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.003274 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 0.5715 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 0.000001295 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0002815 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0009568 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.8229 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) organic substance catabolic process 0.09853 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.6687 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.4355 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.993 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4222 Moderately Informative Inherited
Biological Process (BP) reproduction 0.889 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.9091 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.9341 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.00166 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2639 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.08917 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0.000000004776 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.000000005809 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000003833 Informative Direct
Biological Process (BP) protein catabolic process 0.000004026 Informative Direct
Biological Process (BP) phosphorylation 0.0001417 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0004194 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0009426 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.2582 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.3745 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2349 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.1035 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.1079 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.3229 Informative Inherited
Biological Process (BP) response to nutrient levels 0.1072 Informative Inherited
Biological Process (BP) proteolysis 0.001285 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.07989 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.3694 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 1 Informative Inherited
Biological Process (BP) nitrogen compound transport 0.001004 Informative Inherited
Biological Process (BP) establishment of RNA localization 0.0000000000001302 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.00000000002993 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.00000000004273 Highly Informative Direct
Biological Process (BP) nuclear export 0.0000000002017 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0.000000001138 Highly Informative Direct
Biological Process (BP) regulation of proteolysis 0.00000002352 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 0.00003222 Highly Informative Direct
Biological Process (BP) autophagy 0.0003353 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0003579 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.002507 Highly Informative Inherited
Biological Process (BP) cellular response to starvation 0.215 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.004488 Highly Informative Inherited
Molecular Function (MF) binding 0.00005749 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.8723 Least Informative Inherited
Molecular Function (MF) cation binding 0.6248 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.006265 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.04152 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.0006922 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 1 Informative Inherited
Molecular Function (MF) enzyme binding 0.01075 Informative Inherited
Molecular Function (MF) ligase activity 0.04018 Informative Inherited
Molecular Function (MF) peptidase activity 0.001759 Informative Inherited
Molecular Function (MF) RNA binding 0.03464 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 0.0000000005518 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.00001195 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.0004788 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 0.0006836 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.0008423 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.05284 Highly Informative Inherited
Molecular Function (MF) protein domain specific binding 0.00682 Highly Informative Inherited
Molecular Function (MF) kinase binding 0.01532 Highly Informative Inherited
Molecular Function (MF) structure-specific DNA binding 0.002991 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 0.1377 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.03368 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.3079 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000007176 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0002054 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.07518 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.03494 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.00004325 Informative Direct
Cellular Component (CC) integral to membrane 1 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.9429 Informative Inherited
Cellular Component (CC) nuclear body 0.000002169 Highly Informative Direct
Cellular Component (CC) pore complex 0.00001439 Highly Informative Direct
Cellular Component (CC) cytoplasmic mRNA processing body 0.00004347 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)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 ]