SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (2,955) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 31,299 231,029 111
Proteins 31,015 229,893 111


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)response to stimulus0.97511Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.17990.0000007559Least InformativeInherited
Biological Process (BP)biosynthetic process0.45440.0000002376Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.15310.1816Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.10490.00000000000001079Least InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0036490Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0019750Moderately InformativeInherited
Biological Process (BP)aminoglycan biosynthetic process0.0000000002220Highly InformativeDirect
Biological Process (BP)glycosaminoglycan metabolic process0.0000000000047260Highly InformativeDirect
Biological Process (BP)cell wall biogenesis0.000000070880Highly InformativeDirect
Biological Process (BP)cell wall macromolecule metabolic process0.000000006520Highly InformativeDirect
Biological Process (BP)response to antibiotic0.0000039070.000000006226Highly InformativeDirect
Biological Process (BP)cellular component macromolecule biosynthetic process0.00000000003350Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.00000025320Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)small molecule binding0.19430.000000000000009279Moderately InformativeInherited
Molecular Function (MF)anion binding0.20810.0000000000008469Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.00000000015480InformativeDirect
Molecular Function (MF)carboxylic acid binding0.00080250InformativeDirect
Molecular Function (MF)amide binding0.000083930InformativeDirect
Molecular Function (MF)sulfur compound binding0.00017480InformativeDirect
Molecular Function (MF)peptidase activity, acting on L-amino acid peptides0.8990.958InformativeInherited
Molecular Function (MF)drug binding0.000014120Highly InformativeDirect
Molecular Function (MF)monocarboxylic acid binding0.00019040Highly InformativeDirect
Molecular Function (MF)exopeptidase activity0.0018410.000000000000003188Highly InformativeInherited

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) biosynthetic process 0.0000002376 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0000007559 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000000000001079 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.2705 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.1816 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00004601 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.9181 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.5575 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.03741 Informative Inherited
Biological Process (BP) aminoglycan biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of cell shape 0.00000006471 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) response to antibiotic 0.000000006226 Highly Informative Direct
Biological Process (BP) cellular component macromolecule biosynthetic process 0 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.000000000000009279 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000000000008469 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0 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) peptidase activity, acting on L-amino acid peptides 0.958 Informative Inherited
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) exopeptidase activity 0.000000000000003188 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.0000000002258 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.002776Moderately InformativeInherited
Biological processAntibiotic resistance0InformativeDirect
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processSporulation0.0000005392InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processSeptation0.0000009428Highly InformativeDirect
Cellular componentMembrane0.000007841Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeriplasm0.00000000009486InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0.6158Least InformativeInherited
DomainSignal-anchor0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationProtease0.0004216Moderately InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationCarboxypeptidase0Highly InformativeDirect

Document: KW 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) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]