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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 (3,213) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 19,373 55,987 45
Proteins 17,791 52,568 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) macromolecule metabolic process 0.0000000000009447 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00003664 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.000000001909 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0000001654 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0000005834 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0000007966 Moderately Informative Direct
Biological Process (BP) nitrogen compound transport 0.0001063 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0004398 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.2434 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3383 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.778 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.003501 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.2041 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.2106 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.07287 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.9712 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.5814 Moderately Informative Inherited
Biological Process (BP) reproduction 0.9948 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.05939 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.7236 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.774 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of catabolic process 0 Informative Direct
Biological Process (BP) proteolysis 0.000000000002204 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000000002212 Informative Direct
Biological Process (BP) regulation of proteolysis 0.0000003212 Informative Direct
Biological Process (BP) phosphorylation 0.0004674 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.3609 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.1113 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) regulation of transmembrane transport 0.03581 Informative Inherited
Biological Process (BP) regulation of ion transport 0.2039 Informative Inherited
Biological Process (BP) intracellular transport 0.01956 Informative Inherited
Biological Process (BP) protein transport 0.00153 Informative Inherited
Biological Process (BP) epithelium development 0.7933 Informative Inherited
Biological Process (BP) embryo development 0.8196 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.6807 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.1543 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.6139 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.0212 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.3017 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.5754 Informative Inherited
Biological Process (BP) establishment of RNA localization 0 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex localization 0.00000000001734 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.00000000004248 Highly Informative Direct
Biological Process (BP) nuclear export 0.000000001008 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.00000000473 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 0.0000006231 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.000001562 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 0.000005338 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.00006439 Highly Informative Direct
Biological Process (BP) autophagy 0.00009392 Highly Informative Direct
Biological Process (BP) negative regulation of catabolic process 0.0003303 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0007246 Highly Informative Direct
Biological Process (BP) positive regulation of proteolysis 0.006365 Highly Informative Inherited
Biological Process (BP) regulation of calcium ion transport 0.005031 Highly Informative Inherited
Biological Process (BP) regulation of cation transmembrane transport 0.01429 Highly Informative Inherited
Biological Process (BP) gastrulation 0.01186 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.4753 Highly Informative Inherited
Biological Process (BP) negative regulation of transferase activity 0.002942 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.009901 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphate metabolic process 0.02046 Highly Informative Inherited
Molecular Function (MF) binding 0.00000008084 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.8662 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.8521 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.004177 Moderately Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.0006481 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.08495 Informative Inherited
Molecular Function (MF) enzyme binding 0.00312 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) ubiquitin-like protein transferase activity 0.00000001143 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.000006466 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.0000279 Highly Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 0.0005974 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.001382 Highly Informative Inherited
Molecular Function (MF) protein domain specific binding 0.01742 Highly Informative Inherited
Molecular Function (MF) kinase binding 0.01902 Highly Informative Inherited
Cellular Component (CC) protein complex 0.003589 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.7902 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01866 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0002335 Moderately Informative Direct
Cellular Component (CC) vacuole 0.01101 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.1013 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.00009027 Informative Direct
Cellular Component (CC) ribonucleoprotein granule 0.01892 Informative Inherited
Cellular Component (CC) P-body 0.00007412 Highly Informative Direct
Cellular Component (CC) peptidase complex 0.001506 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processUbl conjugation pathway0Moderately InformativeDirect
Biological processProtein transport0.000000000001024Moderately InformativeDirect
Biological processImmunity0.0008072Moderately InformativeDirect
Biological processDifferentiation0.3915Moderately InformativeInherited
Biological processAutophagy0InformativeDirect
Biological processProtein biosynthesis0InformativeDirect
Biological processInflammatory response0.0000002357InformativeDirect
Biological processmRNA transport0.000000001501Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentLipid droplet0.00000639Highly InformativeDirect
Cellular componentProteasome0.0001539Highly InformativeDirect
DomainLeucine-rich repeat0.0004431InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationProtease0.8374Moderately InformativeInherited
Post-translational modificationThiol protease0.000000003964InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.000005223Least InformativeDirect
Post-translational modificationUbl conjugation0.00009571Moderately InformativeDirect
Post-translational modificationNitration0.000058InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]