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 (2,672) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,484 40,493 11
Proteins 10,371 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)regulation of cellular process0.79921Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.80481Least InformativeInherited
Biological Process (BP)biosynthetic process0.15630.8875Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.05371Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.14921Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.16741Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process3.717e-101.35e-06Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process4.845e-157.593e-11Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process6.178e-070.0001496Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process1.825e-131.137e-12Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process3.761e-141.283e-09Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process09.287e-13Moderately InformativeDirect
Biological Process (BP)positive regulation of molecular function0.12760.1577Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.18161Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.096061Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.17751Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.14151Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.27410.08272Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)RNA metabolic process11Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process00InformativeDirect
Biological Process (BP)ncRNA metabolic process2.817e-085.771e-05InformativeDirect
Biological Process (BP)protein modification by small protein conjugation or removal00InformativeDirect
Biological Process (BP)RNA processing2.038e-060.003369InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.9591InformativeInherited
Biological Process (BP)RNA modification0.020610.02996InformativeInherited
Biological Process (BP)tRNA modification7.815e-132.736e-11Highly InformativeDirect
Biological Process (BP)molybdopterin cofactor metabolic process00Highly InformativeDirect
Biological Process (BP)positive regulation of sequence-specific DNA binding transcription factor activity0.00038353.285e-05Highly InformativeDirect
Molecular Function (MF)transferase activity0.30261Least InformativeInherited
Molecular Function (MF)binding0.48561Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.44971Moderately InformativeInherited
Molecular Function (MF)nucleotidyltransferase activity3.687e-111.647e-08InformativeDirect
Molecular Function (MF)protein dimerization activity0.052720.05666InformativeInherited
Molecular Function (MF)enzyme binding0.01450.0293InformativeInherited
Molecular Function (MF)sulfurtransferase activity1.993e-113.079e-13Highly InformativeDirect
Molecular Function (MF)protein heterodimerization activity1.592e-070.0004284Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.46170.4856Least InformativeInherited
Cellular Component (CC)protein complex0.61461Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.90160.5041Least InformativeInherited
Cellular Component (CC)cytosol1.44e-085.181e-10Moderately InformativeDirect
Cellular Component (CC)nuclear part0.00027960.02527Moderately 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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8875 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 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 aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1.35e-06 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 7.593e-11 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.0001496 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 1.137e-12 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 1.283e-09 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 9.287e-13 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.9219 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.4851 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.8882 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.8294 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1577 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4138 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.4961 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.4515 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.4299 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.5479 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.08272 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.03344 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0 Informative Direct
Biological Process (BP) response to nutrient levels 2.831e-06 Informative Direct
Biological Process (BP) ncRNA metabolic process 5.771e-05 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) positive regulation of transport 0.05409 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.06419 Informative Inherited
Biological Process (BP) regulation of secretion 0.03058 Informative Inherited
Biological Process (BP) muscle structure development 0.09967 Informative Inherited
Biological Process (BP) cardiovascular system development 0.2443 Informative Inherited
Biological Process (BP) muscle tissue development 0.01814 Informative Inherited
Biological Process (BP) RNA processing 0.003369 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.1261 Informative Inherited
Biological Process (BP) cell projection organization 0.349 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.6072 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) central nervous system development 0.07868 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.8383 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) protein catabolic process 0.2416 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) single-organism behavior 0.1075 Informative Inherited
Biological Process (BP) RNA modification 0.02996 Informative Inherited
Biological Process (BP) tRNA modification 2.736e-11 Highly Informative Direct
Biological Process (BP) autophagy 1.576e-13 Highly Informative Direct
Biological Process (BP) cellular response to starvation 0.0003205 Highly Informative Direct
Biological Process (BP) post-embryonic development 2.595e-07 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.0003989 Highly Informative Direct
Biological Process (BP) regulation of autophagy 2.519e-05 Highly Informative Direct
Biological Process (BP) telencephalon development 0.0004121 Highly Informative Direct
Biological Process (BP) adult behavior 0.0008987 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 4.982e-05 Highly Informative Direct
Biological Process (BP) cardiocyte differentiation 7.33e-05 Highly Informative Direct
Biological Process (BP) molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) cardiac muscle tissue development 0.0002078 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 3.285e-05 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.07726 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.1768 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.2583 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.1511 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.005042 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 1.647e-08 Informative Direct
Molecular Function (MF) protein dimerization activity 0.05666 Informative Inherited
Molecular Function (MF) enzyme binding 0.0293 Informative Inherited
Molecular Function (MF) sulfurtransferase activity 3.079e-13 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0004284 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.4856 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.5041 Least Informative Inherited
Cellular Component (CC) cytosol 5.181e-10 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.02527 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 variant5.257e-05Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.009157Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant9.818e-06Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0001747Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0004242Moderately InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant8.996e-05InformativeDirect
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 defective6.601e-06InformativeDirect

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 processTransport0.3598Least InformativeInherited
Biological processProtein transport0Moderately InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processAutophagy0Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentNucleus2.856e-06Least InformativeDirect
Cellular componentCytoplasm1.939e-05Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding5.021e-15Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationTransferase5.452e-05Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAcetylation4.808e-10Least InformativeDirect
Post-translational modificationUbl conjugation1.388e-07Moderately InformativeDirect

Document: KW 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) ]

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) · Internal database links ]