SUPERFAMILY 1.75 HMM library and genome assignments server


Duplicated hybrid motif superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Barrel-sandwich hybrid [ 51229] (4)
Superfamily:   Duplicated hybrid motif [ 51261] (2)
Families:   Glucose permease-like [ 51262] (2)
  Peptidoglycan hydrolase LytM [ 102006]


Superfamily statistics
Genomes (2,424) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,686 104,766 5
Proteins 12,651 104,574 5


Functional annotation
General category Metabolism
Detailed category Carbohydrate metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1.515e-06Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)Protein-N(pi)-phosphohistidine--sugar phosphotrans0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.4232Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1.144e-06Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)Protein-N(pi)-phosphohistidine--sugar phosphotransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processCell wall biogenesis/degradation6.88e-08InformativeDirect
Biological processVirulence7.948e-07InformativeDirect
Biological processPhosphotransferase system0Highly InformativeDirect
Biological processSugar transport0Highly InformativeDirect
Cellular componentMembrane2.12e-12Least InformativeDirect
Cellular componentCell membrane4.301e-10Moderately InformativeDirect
DomainTransmembrane2.785e-06Least InformativeDirect
Molecular functionZinc4.872e-05Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.1049Least InformativeInherited
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationProtease1.322e-12Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationZymogen3.208e-07InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011055 SSF51261 Protein matches
Abstract

The duplicated hybrid motif is a structural motif that is found in certain glucose-permease-like enzymes, and consists of a half-barrel beta-sheet of eight strands that is sandwiched with two 3-stranded beta-sheets. Enzymes displaying this motif include domain IIa of the glucose-specific permease from bacteria , which is part of the phosphoenolpyruvate:sugar phosphotransfer system (PTS), a bacterial and mycoplasma system responsible for the uptake of some sugars and their concomitant phosphorylation [PubMed9705652].

This structural motif is also found in peptidoglycan hydrolase LytM, a member of peptidase family M23, although it contains an extra N-terminal, non-conserved beta-sheet subdomain.


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 · Enzyme Commission (EC) · 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 4 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 Duplicated hybrid motif 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 4 hidden Markov models representing the Duplicated hybrid motif 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 · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]