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ADC-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Double psi beta-barrel [ 50684] (2)
Superfamily:   ADC-like [ 50692] (3)
Families:   Pyruvoyl dependent aspartate decarboxylase, ADC [ 50693]
  Formate dehydrogenase/DMSO reductase, C-terminal domain [ 50696] (10)
  Cdc48 N-terminal domain-like [ 50708] (4)


Superfamily statistics
Genomes (2,543) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,291 71,209 42
Proteins 13,286 71,196 42


Functional annotation
General category General
Detailed category General

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) single-organism metabolic process 0.000000002139 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000003709 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.6556 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.003203 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.1691 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.9892 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9885 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.6193 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.000000000001916 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00000005729 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0002398 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0003205 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0003475 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0004638 Moderately Informative Direct
Biological Process (BP) single-organism transport 0.043 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.03168 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.06454 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.07289 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.4052 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.03628 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.214 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2999 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1831 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1332 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.5067 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.0013 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.5642 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.06123 Moderately Informative Inherited
Biological Process (BP) cellular respiration 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0000000196 Informative Direct
Biological Process (BP) proteolysis 0.0000002328 Informative Direct
Biological Process (BP) protein transport 0.00001297 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.00003224 Informative Direct
Biological Process (BP) single-organism membrane organization 0.00004002 Informative Direct
Biological Process (BP) response to nitrogen compound 0.00004781 Informative Direct
Biological Process (BP) single-organism cellular localization 0.00005295 Informative Direct
Biological Process (BP) intracellular transport 0.00009637 Informative Direct
Biological Process (BP) electron transport chain 0.0001608 Informative Direct
Biological Process (BP) DNA metabolic process 0.02491 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.005481 Informative Inherited
Biological Process (BP) cell development 0.4024 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.003829 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.386 Informative Inherited
Biological Process (BP) cellular component disassembly 0.000000000000007296 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.0000000002116 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0000000008111 Highly Informative Direct
Biological Process (BP) autophagy 0.0000001121 Highly Informative Direct
Biological Process (BP) macromolecule glycosylation 0.0000006313 Highly Informative Direct
Biological Process (BP) pigmentation 0.0000007087 Highly Informative Direct
Biological Process (BP) organelle fusion 0.000001408 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.000005954 Highly Informative Direct
Biological Process (BP) glycoprotein metabolic process 0.00003753 Highly Informative Direct
Biological Process (BP) gliogenesis 0.0000612 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0.00007692 Highly Informative Direct
Biological Process (BP) single-organism membrane fusion 0.001252 Highly Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0.001684 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 0.02818 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.2763 Least Informative Inherited
Molecular Function (MF) binding 0.1018 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.000000000000006264 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0.00000000002778 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.143 Moderately Informative Inherited
Molecular Function (MF) ATPase activity 0 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.0002665 Informative Direct
Molecular Function (MF) iron-sulfur cluster binding 0.000000001988 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.0007886 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.2136 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.3426 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.03442 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6497 Least Informative Inherited
Cellular Component (CC) vacuole 0.001156 Moderately Informative Inherited
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) microbody 0.0000005175 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0005469 Informative Direct
Cellular Component (CC) chromosome 0.005635 Informative Inherited
Cellular Component (CC) lytic vacuole 0.05849 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides1Least InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.5931Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH0.2132Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.8366Moderately InformativeInherited
Enzyme Commission (EC)With other acceptors0.00001206InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.7643InformativeInherited
Enzyme Commission (EC)Nitrate reductase0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Thymidine phosphorylase0.00000000005855Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)0.000002852Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0.3666Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processAutophagy0.0002293InformativeDirect
Biological processNitrate assimilation0Highly InformativeDirect
Cellular componentCytoplasm0.0000000000004123Least InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Coding sequence diversitySelenocysteine0.000000008089InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionIron0Moderately InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionMolybdenum0InformativeDirect
Molecular function2Fe-2S0.000000000000008301InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Molecular functionSchiff base0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationAutocatalytic cleavage0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009010 SSF50692 Protein matches
Abstract

Beta barrels are commonly observed in protein structures. They are classified in terms of two integral parameters: the number of strands in the sheet, n, and the shear number, S, a measure of the stagger of the strands in the beta-sheet. These two parameters have been shown to determine the major geometrical features of beta-barrels. Six-stranded beta-barrels with a pseudo-twofold axis are found in several proteins. One involving parallel strands forming two psi structures is known as the double-psi barrel. The first psi structure consists of the loop connecting strands beta1 and beta2 (a 'psi loop') and the strand beta5, whereas the second psi structure consists of the loop connecting strands beta4 and beta5 and the strand beta2. All the psi structures in double-psi barrels have a unique handedness, in that beta1 (beta4), beta2 (beta5) and the loop following beta5 (beta2) form a right-handed helix. The unique handedness may be related to the fact that the twisting angle between the parallel pair of strands is always larger than that between the antiparallel pair [PubMed10368289].

In many cases, including aspartate decarboxylase and aspartic proteinases, strands 1 and 4 are each bent and consist of two sections. The two sections normally make a right angle; sometimes their hydrogen-bond patterns are disrupted at the corner by a bulge or even by a large insertion. In these cases, the barrel can also be viewed as a pair of orthogonally packed sheets, each with four strands.


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 19 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 ADC-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 19 hidden Markov models representing the ADC-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 ]