SUPERFAMILY 1.75 HMM library and genome assignments server


beta-lactamase/transpeptidase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   beta-lactamase/transpeptidase-like [ 56600]
Superfamily:   beta-lactamase/transpeptidase-like [ 56601] (3)
Families:   beta-Lactamase/D-ala carboxypeptidase [ 56602] (18)
  Glutaminase [ 90084] (2)
  Dac-like [ 144040] (3)


Superfamily statistics
Genomes (2,947) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 31,178 201,590 111
Proteins 30,894 200,880 111


Functional annotation
General category Metabolism
Detailed category Other enzymes

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)cellular macromolecule metabolic process0.88240.8603Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.61250.06506Least InformativeInherited
Biological Process (BP)biosynthetic process0.66330.0009162Least InformativeInherited
Biological Process (BP)single-organism cellular process0.99681Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.17345.072e-05Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.065892.827e-05Least InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.019742.958e-07Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.055052.075e-08Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.09840.1485Moderately InformativeInherited
Biological Process (BP)organonitrogen compound catabolic process0.031310.3127Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.20730.006897Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.19789.251e-11Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0077114.155e-11Moderately InformativeInherited
Biological Process (BP)carboxylic acid catabolic process0.028050.0001982InformativeInherited
Biological Process (BP)aminoglycan biosynthetic process5.379e-090Highly InformativeDirect
Biological Process (BP)glutamine family amino acid catabolic process8.996e-064.595e-08Highly InformativeDirect
Biological Process (BP)glycosaminoglycan metabolic process2.149e-110Highly InformativeDirect
Biological Process (BP)cell wall biogenesis1.514e-070Highly InformativeDirect
Biological Process (BP)cell wall macromolecule metabolic process4.218e-070Highly InformativeDirect
Biological Process (BP)cellular component macromolecule biosynthetic process4.117e-090Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.00013524.364e-09Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)anion binding0.13433.858e-08Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds3.427e-075.819e-10InformativeDirect
Molecular Function (MF)carboxylic acid binding0.0005890InformativeDirect
Molecular Function (MF)amide binding2.925e-050InformativeDirect
Molecular Function (MF)sulfur compound binding4.507e-050InformativeDirect
Molecular Function (MF)drug binding1.29e-050Highly InformativeDirect
Molecular Function (MF)monocarboxylic acid binding5.288e-050Highly 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) nitrogen compound metabolic process 2.827e-05 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0009162 Least Informative Direct
Biological Process (BP) single-organism metabolic process 5.072e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.8603 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.06506 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 2.958e-07 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 2.075e-08 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 4.155e-11 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 9.251e-11 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.8412 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.4196 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.3127 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1485 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6908 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8954 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.006897 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.4969 Moderately Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.0001982 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.02559 Informative Inherited
Biological Process (BP) organ morphogenesis 0.06785 Informative Inherited
Biological Process (BP) regulation of system process 0.05427 Informative Inherited
Biological Process (BP) aminoglycan biosynthetic process 0 Highly Informative Direct
Biological Process (BP) glutamine family amino acid catabolic process 4.595e-08 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.0002268 Highly Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 0 Highly Informative Direct
Biological Process (BP) cell wall biogenesis 0 Highly Informative Direct
Biological Process (BP) cell wall macromolecule metabolic process 0 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 5.598e-05 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.0001246 Highly Informative Direct
Biological Process (BP) cellular component macromolecule biosynthetic process 0 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.01133 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 4.364e-09 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 3.858e-08 Moderately Informative Direct
Molecular Function (MF) peptidase activity 4.431e-06 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 5.819e-10 Informative Direct
Molecular Function (MF) carboxylic acid binding 0 Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) exopeptidase activity 8.13e-13 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 4.064e-07 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 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)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)In linear amides2.368e-16Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.259Moderately InformativeInherited
Enzyme Commission (EC)In cyclic amides0InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.001912InformativeInherited
Enzyme Commission (EC)Serine-type carboxypeptidases0Highly InformativeDirect
Enzyme Commission (EC)Peptidoglycan glycosyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Beta-lactamase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)pericellular component development variant4.838e-05Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant1.99e-05InformativeDirect

Document: WP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.1509Moderately InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Moderately InformativeInherited
Enzyme Commission (EC)In linear amides6.615e-15InformativeDirect
Enzyme Commission (EC)Hexosyltransferases1.254e-05InformativeDirect
Enzyme Commission (EC)In cyclic amides0Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.00179Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.001063Moderately InformativeInherited
Biological processAntibiotic resistance0InformativeDirect
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processSporulation2.22e-07InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Cellular componentMembrane5.505e-06Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeriplasm4.68e-10InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0.9659Least InformativeInherited
DomainSignal-anchor0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationCarboxypeptidase4.026e-14Highly InformativeDirect
Post-translational modificationAminopeptidase0.0003213Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)cell wall biogenesis0InformativeDirect
UniPathway (UP)peptidoglycan biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR012338 SSF56601 Protein matches
Abstract

This entry represents a beta-lactamase structural motif, which contins a cluster of alpha-helices and an alpha/beta sandwich. In addition to beta-lactamases, this domain is also found in D-ala carboxypeptidase/transpeptidase, esterase (EstB) [PubMed11847270], the penicillin receptor BlaR (C-terminal domain), D-aminopeptidase (N-terminal domain) [PubMed10986464], penicillin-biding proteins (e.g. PBP2x, PBP5), and in glutaminase (GlnA). Beta-lactamases are the most common bacterial resistance mechanism against beta-lactam antibiotics [PubMed12945052]. Beta-lactamases appear to have evolved from DD-transpeptidases, which are penicillin-binding proteins involved in cell wall biosynthesis, and as such are one of the main targets of beta-lactam antibiotics.


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) · 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 43 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 beta-lactamase/transpeptidase-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 43 hidden Markov models representing the beta-lactamase/transpeptidase-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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]