SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,526) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 13,201 85,394 42
Proteins 13,198 85,389 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 1.233e-09 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 4.663e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.08932 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01406 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.03742 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 0.005857 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01558 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1223 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9713 Least Informative Inherited
Biological Process (BP) response to stimulus 0.8169 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1.039e-07 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 2.52e-10 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0001127 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 4.408e-08 Moderately Informative Direct
Biological Process (BP) cellular localization 6.432e-06 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 1.905e-08 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0002924 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 3.675e-11 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.03467 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.01769 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.027 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.2005 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.3416 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.178 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.3073 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.0874 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.1694 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.04397 Moderately Informative Inherited
Biological Process (BP) proteolysis 2.229e-09 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0 Informative Direct
Biological Process (BP) protein transport 1.491e-05 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 9.365e-05 Informative Direct
Biological Process (BP) cellular membrane organization 2.654e-05 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001643 Informative Direct
Biological Process (BP) protein catabolic process 7.168e-12 Informative Direct
Biological Process (BP) secretion by cell 0.0004843 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 9.874e-11 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 3.388e-08 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 2.804e-11 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.0001906 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 6.4e-10 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 1.988e-10 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.1176 Informative Inherited
Biological Process (BP) DNA metabolic process 0.006208 Informative Inherited
Biological Process (BP) double-strand break repair 6.349e-08 Highly Informative Direct
Biological Process (BP) protein glycosylation 1.426e-09 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 1.29e-13 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 2.268e-05 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.0002243 Highly Informative Direct
Biological Process (BP) protein ubiquitination 1.548e-05 Highly Informative Direct
Biological Process (BP) ATP metabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) organelle fusion 1.136e-06 Highly Informative Direct
Molecular Function (MF) binding 0.001008 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.01873 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.0003489 Moderately Informative Direct
Molecular Function (MF) cation binding 0.06048 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 1.021e-07 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 8.125e-14 Informative Direct
Molecular Function (MF) transition metal ion binding 6.54e-06 Informative Direct
Molecular Function (MF) protein complex binding 0.0002154 Highly Informative Direct
Molecular Function (MF) metal cluster binding 1.187e-08 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.04152 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.02024 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.5877 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.05047 Least Informative Inherited
Cellular Component (CC) external encapsulating structure 0.0001236 Informative Direct
Cellular Component (CC) chromosome 0.00158 Informative Inherited
Cellular Component (CC) lytic vacuole 0.08958 Informative Inherited
Cellular Component (CC) lysosome 0.0001727 Highly Informative Direct

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 acceptors1.206e-05InformativeDirect
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 phosphorylase5.855e-11Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)2.852e-06Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0.3666Highly InformativeInherited

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.004687Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.01092Least InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant7.425e-05Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal7.753e-05Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant9.095e-05Moderately InformativeDirect
Worm Phenotype (WP)protein aggregation variant0.000176Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0002493Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant0.0009551Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00121Moderately InformativeInherited
Worm Phenotype (WP)endoplasmic reticulum morphology variant6.947e-11Highly InformativeDirect
Worm Phenotype (WP)nuclear number variant1.782e-07Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)neuroanatomy defective0Moderately InformativeDirect
Fly Phenotype (FP)lethal - all die before end of P-stage0Moderately 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)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)anatomical group0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)head0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0InformativeDirect
Enzyme Commission (EC)Acting on NADH or NADPH0.384InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.6335InformativeInherited
Enzyme Commission (EC)Pentosyltransferases0.7555InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.9621InformativeInherited
Enzyme Commission (EC)Formate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.0002499Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0.389Highly 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 processNitrate assimilation0Highly InformativeDirect
Cellular componentCytoplasm1.175e-12Least InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Coding sequence diversitySelenocysteine2.142e-07InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0.5515Least InformativeInherited
Molecular functionIron0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionMolybdenum0InformativeDirect
Molecular function2Fe-2S7.369e-14InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Molecular functionSchiff base0Highly InformativeDirect
Molecular functionUbiquinone6.67e-05Highly InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect
Post-translational modificationAutocatalytic cleavage0InformativeDirect
Post-translational modificationZymogen0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)nitrogen metabolism0.138Moderately InformativeInherited
UniPathway (UP)energy metabolism0.4612Moderately InformativeInherited
UniPathway (UP)one-carbon metabolism0.8003Moderately InformativeInherited
UniPathway (UP)nitrate reduction1.28e-05InformativeDirect
UniPathway (UP)methanogenesis0.007033InformativeInherited
UniPathway (UP)(R)-pantothenate biosynthesis0Highly InformativeDirect
UniPathway (UP)methanogenesis from CO(2)0.0003513Highly InformativeDirect

Document: UP 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) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 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) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]