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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 (2,679) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,582 40,493 11
Proteins 10,451 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)macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.0000019590.0002561Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.000000000000082820Least InformativeDirect
Biological Process (BP)biosynthetic process0.18970.6431Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.011851Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)biological regulation0.68991Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.055841Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.0000000000000016070.000000000000007367Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.0000000040660.000000002117Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process00Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000000000000011910.0000000000002009Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.26561Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.26141Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.3551Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.49951Moderately InformativeInherited
Biological Process (BP)regulation of molecular function0.47420.7158Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)regulation of response to stimulus0.0046430.04839Moderately InformativeInherited
Biological Process (BP)regulation of signaling0.00045760.02921Moderately InformativeInherited
Biological Process (BP)regulation of cell communication0.00065920.02819Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.78910.5513Moderately InformativeInherited
Biological Process (BP)RNA metabolic process11Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)tRNA metabolic process0.000000000010030.0000000189InformativeDirect
Biological Process (BP)coenzyme biosynthetic process00InformativeDirect
Biological Process (BP)ncRNA processing0.00000000052460.0000005233InformativeDirect
Biological Process (BP)peptidyl-amino acid modification0.0021780.00017InformativeInherited
Biological Process (BP)regulation of transcription, DNA-templated0.13531InformativeInherited
Biological Process (BP)positive regulation of immune response0.021610.005334InformativeInherited
Biological Process (BP)positive regulation of signal transduction0.84320.7039InformativeInherited
Biological Process (BP)regulation of defense response0.60870.07892InformativeInherited
Biological Process (BP)RNA modification0.0065040.004131InformativeInherited
Biological Process (BP)tRNA modification0.000000000000050490.000000000001283Highly InformativeDirect
Biological Process (BP)Mo-molybdopterin cofactor metabolic process00Highly InformativeDirect
Biological Process (BP)protein modification by small protein conjugation00Highly InformativeDirect
Biological Process (BP)regulation of toll-like receptor signaling pathway0.00014650.00000003705Highly InformativeDirect
Biological Process (BP)regulation of sequence-specific DNA binding transcription factor activity0.0014090.0004657Highly InformativeInherited
Molecular Function (MF)binding0.58181Least InformativeInherited
Molecular Function (MF)transferase activity0.13321Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.077691Moderately InformativeInherited
Molecular Function (MF)nucleotidyltransferase activity0.0000000000000013940.00000000003723InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups00InformativeDirect
Molecular Function (MF)ligase activity00InformativeDirect
Molecular Function (MF)protein dimerization activity0.11690.1062InformativeInherited
Molecular Function (MF)enzyme binding0.013550.01115InformativeInherited
Molecular Function (MF)sulfurtransferase activity0.0000000026030.00000000009643Highly InformativeDirect
Molecular Function (MF)protein heterodimerization activity0.00000090830.0003993Highly InformativeDirect
Cellular Component (CC)macromolecular complex0.010060.01591Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.1360.04418Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.95280.6586Least InformativeInherited
Cellular Component (CC)nuclear part0.000089510.0002318Moderately InformativeDirect

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) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0002561 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.6431 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 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) heterocycle biosynthetic process 0.000000000000007367 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.000000002117 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000000000002009 Moderately Informative Direct
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) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.7158 Moderately Informative Inherited
Biological Process (BP) reproduction 0.2564 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.8519 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4269 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.04839 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.02921 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.02819 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.3195 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.5513 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0.0000000189 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0 Informative Direct
Biological Process (BP) post-embryonic development 0.0001753 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.00017 Informative Direct
Biological Process (BP) ncRNA processing 0.0000005233 Informative Direct
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.139 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.08214 Informative Inherited
Biological Process (BP) single organism reproductive process 0.1327 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.09971 Informative Inherited
Biological Process (BP) cell development 0.1244 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.791 Informative Inherited
Biological Process (BP) positive regulation of immune response 0.005334 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.7039 Informative Inherited
Biological Process (BP) regulation of defense response 0.07892 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.03194 Informative Inherited
Biological Process (BP) behavior 0.1103 Informative Inherited
Biological Process (BP) RNA modification 0.004131 Informative Inherited
Biological Process (BP) tRNA modification 0.000000000001283 Highly Informative Direct
Biological Process (BP) autophagy 0.000000004191 Highly Informative Direct
Biological Process (BP) aging 0.00009689 Highly Informative Direct
Biological Process (BP) locomotory behavior 0.0002988 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.00001114 Highly Informative Direct
Biological Process (BP) Mo-molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0 Highly Informative Direct
Biological Process (BP) regulation of toll-like receptor signaling pathway 0.00000003705 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 0.000004619 Highly Informative Direct
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0.0004657 Highly Informative Direct
Biological Process (BP) proteolysis involved in cellular protein catabolic process 0.0002967 Highly Informative Direct
Biological Process (BP) germ cell development 0.003623 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.01111 Highly Informative Inherited
Biological Process (BP) positive regulation of catabolic process 0.001865 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 0.00000000003723 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.1062 Informative Inherited
Molecular Function (MF) enzyme binding 0.01115 Informative Inherited
Molecular Function (MF) sulfurtransferase activity 0.00000000009643 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0003993 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.01591 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.04418 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.6586 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0002318 Moderately Informative Direct

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)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0001551Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0002946Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0008321Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.001531Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.01409Least InformativeInherited
Worm Phenotype (WP)protein protein interaction variant0.000001689Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0001563Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0002309Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0002309Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0005032Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.007584Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.01527Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.1153Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.2205Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.2797Moderately InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.0001357InformativeDirect
Worm Phenotype (WP)protruding vulva0.0001662InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant0.0001764InformativeDirect
Worm Phenotype (WP)brood size variant0.001284InformativeInherited
Worm Phenotype (WP)pattern protein expression variant0.06756InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.1006InformativeInherited
Worm Phenotype (WP)exploded through vulva0.0004512Highly InformativeDirect

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 defective0.000006684InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least 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 phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0.000693Moderately InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0Highly InformativeDirect
Enzyme Commission (EC)Acid--thiol ligases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.3755Least InformativeInherited
Biological processProtein transport0Moderately InformativeDirect
Biological processUbl conjugation pathway0Moderately InformativeDirect
Biological processAutophagy0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentNucleus0.000000003954Least InformativeDirect
Cellular componentCytoplasm0.0000004265Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding0.0000002Least InformativeDirect
Post-translational modificationTransferase0.0001526Least InformativeDirect
Post-translational modificationAcetylation0.0000000002465Least InformativeDirect
Post-translational modificationPhosphoprotein0.000366Least InformativeDirect
Post-translational modificationUbl conjugation0.0000007749Moderately 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 metabolism0.00000003105Least InformativeDirect
UniPathway (UP)tRNA modification0InformativeDirect
UniPathway (UP)molybdopterin biosynthesis0Highly InformativeDirect
UniPathway (UP)protein sumoylation0Highly InformativeDirect
UniPathway (UP)5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis0.00000000156Highly 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) · Zebrafish Anatomy (ZA) · 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) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]