SUPERFAMILY 1.75 HMM library and genome assignments server

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PLP-binding barrel superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   PLP-binding barrel [ 51419] (2)
Families:   Alanine racemase-like, N-terminal domain [ 51420] (3)
  "Hypothetical" protein ybl036c [ 51427]


Superfamily statistics
Genomes (2,981) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,664 85,537 17
Proteins 13,597 85,249 17


Functional annotation
General category Metabolism
Detailed category Amino acids metabolism and transport

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) organonitrogen compound metabolic process 0.000000003664 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00000002289 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.002339 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.02347 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9911 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000000001763 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0006352 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.367 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2414 Moderately Informative Inherited
Biological Process (BP) amine metabolic process 0 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0 Informative Direct
Biological Process (BP) regulation of catabolic process 0.00000000004781 Informative Direct
Biological Process (BP) regulation of transmembrane transport 0.000007551 Informative Direct
Biological Process (BP) positive regulation of transport 0.007103 Informative Inherited
Biological Process (BP) regulation of protein catabolic process 0 Highly Informative Direct
Biological Process (BP) polyamine metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0.00000000006802 Highly Informative Direct
Biological Process (BP) positive regulation of transmembrane transport 0.00000003577 Highly Informative Direct
Biological Process (BP) negative regulation of catabolic process 0.00000004682 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000006 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.00001252 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.003684 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.001758 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.00000000000001973 Informative Direct
Molecular Function (MF) enzyme activator activity 0.0000007773 Informative Direct
Molecular Function (MF) protein dimerization activity 0.00009423 Informative Direct
Molecular Function (MF) identical protein binding 0.0003393 Informative Direct
Molecular Function (MF) vitamin binding 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.000000008217 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.000003504 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on amino acids and derivatives0InformativeDirect
Enzyme Commission (EC)Arginine decarboxylase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.08541Moderately InformativeInherited
Biological processPolyamine biosynthesis0Highly InformativeDirect
Biological processLysine biosynthesis0Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · 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 10 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 PLP-binding 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 10 hidden Markov models representing the PLP-binding 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 · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]