SUPERFAMILY 1.75 HMM library and genome assignments server

Activating enzymes of the ubiquitin-like proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Activating enzymes of the ubiquitin-like proteins [ 69571]
Superfamily:   Activating enzymes of the ubiquitin-like proteins [ 69572] (2)
Families:   Molybdenum cofactor biosynthesis protein MoeB [ 69573]
  Ubiquitin activating enzymes (UBA) [ 89763] (2)


Superfamily statistics
Genomes (2,674) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,508 40,493 11
Proteins 10,390 39,302 11


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)protein metabolic process00Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.16161Least InformativeInherited
Biological Process (BP)regulation of cellular process0.82421Least InformativeInherited
Biological Process (BP)positive regulation of biological process0.88420.8419Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.83441Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.17881Least InformativeInherited
Biological Process (BP)biosynthetic process0.13680.4258Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.064881Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.00000000082890.000003092Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0000000000000063590.0000000000006279Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.0000012080.0002143Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.00000000000064860.000000000002143Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.00000000000005070.00000000001587Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process00.0000000000006975Moderately InformativeDirect
Biological Process (BP)regulation of gene expression0.32581Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.093561Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.17651Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.13851Moderately InformativeInherited
Biological Process (BP)positive regulation of molecular function0.11710.1529Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.27320.08078Moderately InformativeInherited
Biological Process (BP)RNA metabolic process11Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process00InformativeDirect
Biological Process (BP)protein modification by small protein conjugation or removal00InformativeDirect
Biological Process (BP)peptidyl-amino acid modification0.96261InformativeInherited
Biological Process (BP)RNA processing0.0000017330.01957InformativeInherited
Biological Process (BP)RNA modification0.019540.02873InformativeInherited
Biological Process (BP)ncRNA metabolic process0.000000023040.001164InformativeInherited
Biological Process (BP)tRNA modification0.00000000000064770.00000000002497Highly InformativeDirect
Biological Process (BP)molybdopterin cofactor metabolic process00Highly InformativeDirect
Biological Process (BP)positive regulation of sequence-specific DNA binding transcription factor activity0.00037350.00003206Highly InformativeDirect
Molecular Function (MF)binding0.47451Least InformativeInherited
Molecular Function (MF)transferase activity0.40391Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.3671Moderately InformativeInherited
Molecular Function (MF)nucleotidyltransferase activity0.000000000030980.00000001508InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups00InformativeDirect
Molecular Function (MF)protein dimerization activity0.053240.05618InformativeInherited
Molecular Function (MF)enzyme binding0.015060.0305InformativeInherited
Molecular Function (MF)sulfurtransferase activity0.0000000017930.00000000005968Highly InformativeDirect
Molecular Function (MF)protein heterodimerization activity0.00000016140.0004345Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.36670.576Least InformativeInherited
Cellular Component (CC)protein complex0.4310.7737Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.91080.2639Least InformativeInherited
Cellular Component (CC)cytosol0.0000000096070.0000000006679Moderately InformativeDirect
Cellular Component (CC)nuclear part0.00017550.01089Moderately InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) protein metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.8419 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.4258 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.000003092 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0000000000006279 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.0002143 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.000000000002143 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00000000001587 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0000000000006975 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.964 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.7599 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.6712 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.9375 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.4779 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1529 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.08078 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.4889 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.4173 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.5408 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.286 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.03308 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.3059 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.5438 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.163 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.3981 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0 Informative Direct
Biological Process (BP) response to nutrient levels 0.000003684 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) cellular response to external stimulus 0.00007591 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.06439 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.04275 Informative Inherited
Biological Process (BP) regulation of secretion 0.03441 Informative Inherited
Biological Process (BP) positive regulation of transport 0.06537 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.5138 Informative Inherited
Biological Process (BP) muscle structure development 0.06114 Informative Inherited
Biological Process (BP) cardiovascular system development 0.2348 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.8492 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.1154 Informative Inherited
Biological Process (BP) cell projection organization 0.3502 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.6047 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) central nervous system development 0.07895 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) protein catabolic process 0.245 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) positive regulation of catabolic process 0.05386 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.16 Informative Inherited
Biological Process (BP) RNA processing 0.01957 Informative Inherited
Biological Process (BP) single-organism behavior 0.05519 Informative Inherited
Biological Process (BP) RNA modification 0.02873 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.001164 Informative Inherited
Biological Process (BP) gland development 0.03941 Informative Inherited
Biological Process (BP) tRNA modification 0.00000000002497 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0000002159 Highly Informative Direct
Biological Process (BP) regulation of autophagy 0.00003472 Highly Informative Direct
Biological Process (BP) macroautophagy 0.00002555 Highly Informative Direct
Biological Process (BP) telencephalon development 0.0004753 Highly Informative Direct
Biological Process (BP) adult behavior 0.0008611 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 0.00005773 Highly Informative Direct
Biological Process (BP) cardiocyte differentiation 0.00006851 Highly Informative Direct
Biological Process (BP) molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.0006753 Highly Informative Direct
Biological Process (BP) cardiac muscle tissue development 0.0002059 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.00003206 Highly Informative Direct
Biological Process (BP) negative regulation of chromosome organization 0.0001778 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.07151 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.005887 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.2452 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.2504 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.1381 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.005105 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.00000001508 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) ligase activity 0.000001195 Informative Direct
Molecular Function (MF) protein dimerization activity 0.05618 Informative Inherited
Molecular Function (MF) enzyme binding 0.0305 Informative Inherited
Molecular Function (MF) sulfurtransferase activity 0.00000000005968 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0004345 Highly Informative Direct
Cellular Component (CC) protein complex 0.7737 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.576 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2639 Least Informative Inherited
Cellular Component (CC) cytosol 0.0000000006679 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.01089 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00005257Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.009157Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant0.000009818Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0001747Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0004242Moderately InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant0.00008996InformativeDirect
Worm Phenotype (WP)brood size variant0.0004109InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)cell death defective0.000006586InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)developing material anatomical entity0Moderately InformativeDirect
Fly Anatomy (FA)pupa0InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous 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
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately 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)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.3616Least InformativeInherited
Biological processProtein transport0Moderately InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processAutophagy0Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentNucleus0.0000000647Least InformativeDirect
Cellular componentCytoplasm0.000001766Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding0.0000000000000488Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationTransferase0.00006463Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAcetylation0.0000000004838Least InformativeDirect
Post-translational modificationUbl conjugation0.00000015Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism0.00000003431Least InformativeDirect
UniPathway (UP)tRNA modification0InformativeDirect
UniPathway (UP)molybdopterin biosynthesis0Highly InformativeDirect
UniPathway (UP)protein sumoylation0Highly InformativeDirect
UniPathway (UP)5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis0.000000001607Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009036 SSF69572 Protein matches
Abstract

The Escherichia coli protein is involved in molybdenum cofactor (MoCF) biosynthesis, an evolutionarily conserved pathway. MoeB activates the C terminus of MoaD to form an acyl-adenylate, which is subsequently converted to a thiocarboxylate that acts as the sulphur donor during Moco biosynthesis. The structure of MoeB consists of a three-layer sandwich of alpha/beta/alpha [PubMed11713534]. The sandwich is composed of eight beta-strands, which form a continuous mixed beta sheet in the order 32145678 surrounded by eight helices. Beta strands 6 and 8 are antiparallel to the rest. The N-terminal half of the sheet contains the ATP nucleotide-binding site, which is similar to that of the NAD-binding Rossmann fold. A loop between beta-1 and alpha-3 contains a glycine-rich motif similar to the P loop found in enzymes that hydrolyse ATP. The C-terminal half of the sheet contains a fold that is similar to that found in a family of sugar-binding proteins.


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 3 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 Activating enzymes of the ubiquitin-like proteins 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 3 hidden Markov models representing the Activating enzymes of the ubiquitin-like proteins 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]