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 (2,948) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 31,210 201,590 111
Proteins 30,926 200,880 111


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 component organization or biogenesis0.62860.1186Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.87110.7562Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.44330.01729Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.64620.0008544Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.074120.00003375Least InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.019780.000000278Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.055760.00000002463Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.010150.00000000008841Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.10220.1486Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.056170.2357Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.094540.2784Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.19290.005064Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.19360.00000000007241Moderately InformativeInherited
Biological Process (BP)cell wall organization or biogenesis0.00000090480InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.028280.0001486InformativeInherited
Biological Process (BP)organonitrogen compound catabolic process0.030780.285InformativeInherited
Biological Process (BP)aminoglycan biosynthetic process0.000000004080Highly InformativeDirect
Biological Process (BP)glutamine family amino acid catabolic process0.0000089090.00000004595Highly InformativeDirect
Biological Process (BP)glycosaminoglycan metabolic process0.000000000030120Highly InformativeDirect
Biological Process (BP)cell wall macromolecule biosynthetic process0.000000004080.0000001574Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.00013590.00000001268Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)small molecule binding0.097580.0000000007535Moderately InformativeInherited
Molecular Function (MF)anion binding0.13440.00000003856Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.00000033950.0000000003745InformativeDirect
Molecular Function (MF)carboxylic acid binding0.00059020InformativeDirect
Molecular Function (MF)amide binding0.000029210InformativeDirect
Molecular Function (MF)sulfur compound binding0.00008140InformativeDirect
Molecular Function (MF)drug binding0.000012910Highly InformativeDirect
Molecular Function (MF)monocarboxylic acid binding0.000052780Highly 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 0.00003375 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0008544 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.1186 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.7562 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.01729 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.000000278 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.00000002463 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00000000008841 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.00000000007241 Moderately Informative Direct
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.7012 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.4804 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1486 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2784 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.2357 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8843 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.005064 Moderately Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.0001486 Informative Direct
Biological Process (BP) cell wall organization or biogenesis 0 Informative Direct
Biological Process (BP) regulation of system process 0.007717 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.02434 Informative Inherited
Biological Process (BP) organ morphogenesis 0.06594 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.285 Informative Inherited
Biological Process (BP) neurological system process 0.1388 Informative Inherited
Biological Process (BP) aminoglycan biosynthetic process 0 Highly Informative Direct
Biological Process (BP) glutamine family amino acid catabolic process 0.00000004595 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.0002404 Highly Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 0 Highly Informative Direct
Biological Process (BP) cell wall macromolecule biosynthetic process 0.0000001574 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.00005281 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.0005572 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.01082 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00000001268 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.0000000007535 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00000003856 Moderately Informative Direct
Molecular Function (MF) peptidase activity 0.00001287 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.0000000003745 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 0.000000000004182 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.0000003207 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 variant0.00004838Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0.0000199InformativeDirect

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)Glycosyltransferases0.154Moderately InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Moderately InformativeInherited
Enzyme Commission (EC)In linear amides0.000000000000006164InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.00001401InformativeDirect
Enzyme Commission (EC)In cyclic amides0Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.001789Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antiinfectives for systemic use0Least InformativeDirect
Drugbank ATC_code (DB)sensory organs0.7789Least InformativeInherited
Drugbank ATC_code (DB)antibacterials for systemic use0Moderately InformativeDirect
Drugbank ATC_code (DB)antiinfectives0.006739Moderately InformativeInherited
Drugbank ATC_code (DB)other beta-lactam antibacterials0.000000000001391InformativeDirect
Drugbank ATC_code (DB)ampicillin0.0001926Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.000958Moderately InformativeDirect
Biological processAntibiotic resistance0InformativeDirect
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processSporulation0.0000002241InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Cellular componentMembrane0.00000651Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeriplasm0.0000000005059InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0.7035Least InformativeInherited
DomainSignal-anchor0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationCarboxypeptidase0.00000000000004009Highly InformativeDirect
Post-translational modificationAminopeptidase0.0003225Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cell wall metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)peptidoglycan biosynthesis0InformativeDirect

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) · DrugBank ATC (DB) · 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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]