SUPERFAMILY 1.75 HMM library and genome assignments server

L,D-transpeptidase catalytic domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   L,D-transpeptidase catalytic domain-like [ 141522]
Superfamily:   L,D-transpeptidase catalytic domain-like [ 141523]
Families:   L,D-transpeptidase catalytic domain-like [ 141524] (2)


Superfamily statistics
Genomes (1,731) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,229 39,131 2
Proteins 6,229 39,130 2


Functional annotation
General category Metabolism
Detailed category Other enzymes

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 macromolecule metabolic process 0.7741 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8033 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1685 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.7551 Least Informative Inherited
Biological Process (BP) cellular component biogenesis 0.005388 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.01748 Moderately Informative Inherited
Biological Process (BP) cell wall organization or biogenesis 0.00000003529 Informative Direct
Biological Process (BP) proteolysis 0.00001736 Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 0.00000003028 Highly Informative Direct
Molecular Function (MF) transferase activity 0.1949 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.05522 Least Informative Inherited
Molecular Function (MF) peptidase activity 0.000005036 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.000007878 Informative Direct
Molecular Function (MF) exopeptidase activity 0.00000000001018 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring amino-acyl groups 0.00000000001725 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.0000000003294 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Cellular componentPeriplasm0.0000000000004769InformativeDirect
DomainSignal0.0000002118Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.0000002997Least InformativeDirect
Post-translational modificationGlycosyltransferase0.00000000003419InformativeDirect
Post-translational modificationAcyltransferase0.0002986InformativeDirect

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

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 2 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 L,D-transpeptidase catalytic domain-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 2 hidden Markov models representing the L,D-transpeptidase catalytic domain-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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]