SUPERFAMILY 1.75 HMM library and genome assignments server


Dimeric alpha+beta barrel superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Dimeric alpha+beta barrel [ 54909] (23)
Families:   Actinorhodin biosynthesis monooxygenase ActVa-Orf6 [ 82666]
  Plant stress-induced protein [ 89927] (3)
  PG130-like [ 102959] (5)
  Hypothetical protein YjcS [ 102962]
  YciI-like [ 102965]
  Muconalactone isomerase, MLI [ 54910]
  Lrp/AsnC-like transcriptional regulator C-terminal domain [ 69733] (4)
  Polyketide synthesis cyclase [ 110959]
  DGPF domain (Pfam 04946) [ 110962]
  Chlorite dismutase-like [ 110965] (2)
  PA3566-like [ 110970] (5)
  Hypothetical protein YdhR [ 117940]
  NIPSNAP [ 117943] (2)
  Dyp-type peroxidase-like [ 143265] (3)
  EthD-like [ 143272]
  Atu0297-like [ 143275]
  SOR-like [ 143278]
  YbaA-like [ 160289]
  MmlI-like [ 160292]
  Marine metagenome family DABB2 [ 160295]
  YiiL-like [ 160298]
  Marine metagenome family DABB1 [ 160301] (2)
  Marine metagenome family DABB3 [ 160306]


Superfamily statistics
Genomes (2,617) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 28,802 66,440 47
Proteins 27,522 64,669 47


Functional annotation
General category Metabolism
Detailed category Secondary metabolism

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) 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) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.3132 Moderately Informative Inherited
Biological Process (BP) phenol-containing compound metabolic process 0.0001868 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.3657 Moderately Informative Inherited
Molecular Function (MF) tetrapyrrole binding 7.535e-05 Informative Direct
Molecular Function (MF) peroxidase activity 9.021e-06 Highly Informative Direct
Molecular Function (MF) heme binding 5.795e-05 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)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.2323Least InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red5.545e-15Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0InformativeDirect
Enzyme Commission (EC)Miscellaneous (requires further characterization)0InformativeDirect
Enzyme Commission (EC)Transposing C==C bonds1.622e-10InformativeDirect

Document: EC annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)visual 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)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least 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)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least 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.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six 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)Oxidoreductases0.04041Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.3118Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen4.998e-14InformativeDirect
Enzyme Commission (EC)Acting on single donors with incorporation of molecular oxygen0.0001856InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases1InformativeInherited
Enzyme Commission (EC)Miscellaneous (requires further characterization)0Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0Highly InformativeDirect
Enzyme Commission (EC)Transposing C==C bonds1.99e-09Highly InformativeDirect
Enzyme Commission (EC)Acyl groups converted into alkyl on transfer4.899e-05Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processAromatic hydrocarbons catabolism4.471e-09InformativeDirect
Cellular componentCytoplasm5.015e-07Least InformativeDirect
Cellular componentPeriplasm6.863e-10InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0.7429Least InformativeInherited
Molecular functionIron1.186e-08Moderately InformativeDirect
Molecular functionCalcium0.0003465Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationActivator9.367e-09Moderately InformativeDirect
Post-translational modificationOxidoreductase2.657e-07Moderately InformativeDirect
Post-translational modificationRepressor0.0004225Moderately InformativeDirect
Post-translational modificationPeroxidase5.177e-13Highly InformativeDirect
Post-translational modificationMonooxygenase1.287e-11Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism3.988e-08Least InformativeDirect
UniPathway (UP)beta-ketoadipate pathway0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011008 SSF54909 Protein matches
Abstract

Dimeric alpha-beta barrel domains exhibit an alpha+beta sandwich fold with an antiparallel beta sheet that forms a closed barrel. These domains dimerise through the beta-sheet, and in some cases these dimers may assemble into higher oligomers. Domains with this structure are found in proteins from several different families, including bacterial actinorhodin biosynthesis monooxygenase (ActVa-Orf6), which catalyses the oxidation of an aromatic intermediate of the actinorhodin biosynthetic pathway [PubMed12514126]; bacterial muconalactone isomerase, a decamer composed of five dimers [PubMed2926818]; and the C-terminal domain of archaeal LprA, a member of the Lrp/AqsnC family of transcription regulators [PubMed11230123].


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) · 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 41 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 Dimeric alpha+beta barrel 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 41 hidden Markov models representing the Dimeric alpha+beta barrel 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]