SUPERFAMILY 1.75 HMM library and genome assignments server


OmpA-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Bacillus chorismate mutase-like [ 55297] (9)
Superfamily:   OmpA-like [ 103088]
Families:   OmpA-like [ 103089] (2)


Superfamily statistics
Genomes (1,947) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,975 57,361 4
Proteins 9,898 57,151 4


Functional annotation
General category Metabolism
Detailed category Cell envelope metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) transporter activity 0.1366 Moderately Informative Inherited
Cellular Component (CC) membrane 0.007694 Least Informative Inherited
Cellular Component (CC) external encapsulating structure 1.825e-13 Informative Direct
Cellular Component (CC) cell envelope 0 Highly Informative Direct
Cellular Component (CC) external encapsulating structure part 0 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport4.713e-16Moderately InformativeDirect
Biological processChemotaxis2.47e-11InformativeDirect
Biological processConjugation0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell outer membrane0InformativeDirect
DomainSignal2.737e-15Least InformativeDirect
DomainTransmembrane2.679e-09Least InformativeDirect
DomainTransmembrane beta strand0InformativeDirect
Post-translational modificationDisulfide bond0.000145Least InformativeDirect
Post-translational modificationPalmitate4.853e-05Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006665 SSF103088 Protein matches
Abstract

This entry represents domain with a beta/alpha/beta/alpha-beta(2) structure found in the C-terminal region of many Gram-negative bacterial outer membrane proteins [PubMed1538702], such as porin-like integral membrane proteins (such as ompA) [PubMed2202726], small lipid-anchored proteins (such as pal) [PubMed10515919], and MotB proton channels [PubMed17052729]. The N-terminal half is variable although some of the proteins in this group have the OmpA-like transmembrane domain at the N terminus. OmpA from Escherichia coli is required for pathogenesis, and can interact with host receptor molecules [PubMed17368067]. MotB (and MotA) serves two functions in E.coli, the MotA(4)-MotB(2) complex attaches to the cell wall via MotB to form the stator of the flagellar motor, and the MotA-MotB complex couples the flow of ions across the cell membrane to movement of the rotor [PubMed17052729].


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-coverage) · 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 3 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 OmpA-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 3 hidden Markov models representing the OmpA-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-coverage) · UniProtKB KeyWords (KW) · Internal database links ]