SUPERFAMILY 1.75 HMM library and genome assignments server


Helical scaffold and wing domains of SecA superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Helical scaffold and wing domains of SecA [ 81885]
Superfamily:   Helical scaffold and wing domains of SecA [ 81886]
Families:   Helical scaffold and wing domains of SecA [ 81887]


Superfamily statistics
Genomes (2,653) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,165 21,180 3
Proteins 3,128 21,143 3


Functional annotation
General category Processes_IC
Detailed category Protein modification

Document:
Function annotation of SCOP domain superfamilies

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processTranslocation0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Cellular componentThylakoid1.803e-14InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011116 SSF81886 Protein matches
Abstract

SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner. This domain is composed of two C-terminal alpha helical subdomains: the wing and scaffold subdomains.


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 · 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 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 Helical scaffold and wing domains of SecA 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 Helical scaffold and wing domains of SecA 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 · UniProtKB KeyWords (KW) · Internal database links ]