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 (2,628) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 10,944 19,448 11
Proteins 9,960 18,671 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 metabolic process0.70461Least InformativeInherited
Biological Process (BP)regulation of cellular process0.64181Least InformativeInherited
Biological Process (BP)biosynthetic process0.19710.9448Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.042211Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.20381Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.1391Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process3.929e-111.623e-06Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process05.521e-13Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process3.191e-070.0002096Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process4.866e-142.157e-13Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process6.167e-151.181e-11Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process01.931e-15Moderately InformativeDirect
Biological Process (BP)positive regulation of molecular function0.075930.06214Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.13111Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.07031Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.13451Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.10591Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.43040.148Moderately 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 process1.113e-082.327e-05InformativeDirect
Biological Process (BP)RNA processing8.829e-070.001775InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.97451InformativeInherited
Biological Process (BP)RNA modification0.017870.01915InformativeInherited
Biological Process (BP)tRNA modification3.208e-131.294e-11Highly InformativeDirect
Biological Process (BP)molybdopterin cofactor metabolic process00Highly InformativeDirect
Biological Process (BP)positive regulation of sequence-specific DNA binding transcription factor activity0.00050533.425e-05Highly InformativeDirect
Molecular Function (MF)binding0.52381Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.39411Moderately InformativeInherited
Molecular Function (MF)nucleotidyltransferase activity1.116e-115.569e-09InformativeDirect
Molecular Function (MF)protein dimerization activity0.038930.03421InformativeInherited
Molecular Function (MF)sulfurtransferase activity00Highly InformativeDirect
Molecular Function (MF)protein heterodimerization activity9.258e-080.000457Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle10.9954Least InformativeInherited
Cellular Component (CC)protein complex0.49080.8584Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.27480.3301Least InformativeInherited
Cellular Component (CC)cytosol1.287e-092.166e-11Moderately InformativeDirect
Cellular Component (CC)nuclear part0.027180.1039Moderately 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) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.9448 Least Informative Inherited
Biological Process (BP) heterocycle metabolic 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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1.623e-06 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 5.521e-13 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.0002096 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 2.157e-13 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 1.181e-11 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 1.931e-15 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.06214 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 0.8981 Moderately Informative Inherited
Biological Process (BP) macromolecule catabolic process 0.6958 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.148 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 0.0004476 Informative Direct
Biological Process (BP) ncRNA metabolic process 2.327e-05 Informative Direct
Biological Process (BP) RNA processing 0.001775 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 1 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) protein catabolic process 0.5949 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) RNA modification 0.01915 Informative Inherited
Biological Process (BP) tRNA modification 1.294e-11 Highly Informative Direct
Biological Process (BP) autophagy 1.732e-10 Highly Informative Direct
Biological Process (BP) post-embryonic development 1.911e-05 Highly Informative Direct
Biological Process (BP) molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 3.425e-05 Highly Informative Direct
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 5.569e-09 Informative Direct
Molecular Function (MF) protein dimerization activity 0.03421 Informative Inherited
Molecular Function (MF) sulfurtransferase activity 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.000457 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.9954 Least Informative Inherited
Cellular Component (CC) protein complex 0.8584 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3301 Least Informative Inherited
Cellular Component (CC) cytosol 2.166e-11 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1039 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 defective1.418e-06InformativeDirect
Fly Phenotype (FP)cell lethal2.811e-05Highly InformativeDirect

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

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 processTransport0.3613Least InformativeInherited
Biological processProtein transport0Moderately InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processAutophagy0Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentNucleus2.476e-06Least InformativeDirect
Cellular componentCytoplasm1.58e-05Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding2.29e-15Least InformativeDirect
Post-translational modificationTransferase5.765e-05Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAcetylation4.689e-10Least InformativeDirect
Post-translational modificationUbl conjugation1.161e-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 ]