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100  structures 3418  species 1  interaction 17270  sequences 239  architectures

Family: OmpA (PF00691)

Summary: OmpA family

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This is the Wikipedia entry entitled "OmpA domain". More...

OmpA domain Edit Wikipedia article

OmpA family
PDB 2hqs EBI.jpg
crystal structure of tolb/pal complex
Identifiers
Symbol OmpA
Pfam PF00691
InterPro IPR006665
PROSITE PDOC00819
SCOP 1r1m
SUPERFAMILY 1r1m
TCDB 1.B.6

In molecular biology, the OmpA domain is a conserved protein domain with a beta/alpha/beta/alpha-beta(2) structure found in the C-terminal region of many Gram-negative bacterial outer membrane proteins, such as porin-like integral membrane proteins (such as ompA), small lipid-anchored proteins (such as pal), and MotB proton channels.[1][2][3][4] The N-terminal half of these proteins 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.[5] MotB (and MotA) serve 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.[4]

References[edit]

  1. ^ Bouveret E, Benedetti H, Rigal A, Loret E, Lazdunski C (October 1999). "In vitro characterization of peptidoglycan-associated lipoprotein (PAL)-peptidoglycan and PAL-TolB interactions". J. Bacteriol. 181 (20): 6306–11. PMC 103764. PMID 10515919. 
  2. ^ De Mot R, Proost P, Van Damme J, Vanderleyden J (February 1992). "Homology of the root adhesin of Pseudomonas fluorescens OE 28.3 with porin F of P. aeruginosa and P. syringae". Mol. Gen. Genet. 231 (3): 489–93. PMID 1538702. 
  3. ^ Freudl R, Klose M, Henning U (June 1990). "Export and sorting of the Escherichia coli outer membrane protein OmpA". J. Bioenerg. Biomembr. 22 (3): 441–9. doi:10.1007/BF00763176. PMID 2202726. 
  4. ^ a b Hosking ER, Vogt C, Bakker EP, Manson MD (December 2006). "The Escherichia coli MotAB proton channel unplugged". J. Mol. Biol. 364 (5): 921–37. doi:10.1016/j.jmb.2006.09.035. PMID 17052729. 
  5. ^ Selvaraj SK, Periandythevar P, Prasadarao NV (April 2007). "Outer membrane protein A of Escherichia coli K1 selectively enhances the expression of intercellular adhesion molecule-1 in brain microvascular endothelial cells". Microbes Infect. 9 (5): 547–57. doi:10.1016/j.micinf.2007.01.020. PMC 1993839. PMID 17368067. 

This article incorporates text from the public domain Pfam and InterPro IPR006665

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

OmpA family Provide feedback

The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006665

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 [PUBMED:1538702], such as porin-like integral membrane proteins (such as ompA) [PUBMED:2202726], small lipid-anchored proteins (such as pal) [PUBMED:10515919], and MotB proton channels [PUBMED:17052729]. The N-terminal half is variable although some of the proteins in this group have the OmpA-like transmembrane domain INTERPRO at the N terminus. OmpA from Escherichia coli is required for pathogenesis, and can interact with host receptor molecules [PUBMED:17368067]. 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 [PUBMED:17052729].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(84)
Full
(17270)
Representative proteomes NCBI
(13311)
Meta
(4143)
RP15
(1365)
RP35
(2716)
RP55
(3618)
RP75
(4376)
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Format an alignment

  Seed
(84)
Full
(17270)
Representative proteomes NCBI
(13311)
Meta
(4143)
RP15
(1365)
RP35
(2716)
RP55
(3618)
RP75
(4376)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(84)
Full
(17270)
Representative proteomes NCBI
(13311)
Meta
(4143)
RP15
(1365)
RP35
(2716)
RP55
(3618)
RP75
(4376)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_166 (release 2.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 84
Number in full: 17270
Average length of the domain: 97.50 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 31.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 97
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

PD40

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the OmpA domain has been found. There are 100 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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