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9  structures 841  species 0  interactions 1301  sequences 16  architectures

Family: OmpA_membrane (PF01389)

Summary: OmpA-like transmembrane domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "OmpA-like transmembrane domain". More...

OmpA-like transmembrane domain Edit Wikipedia article

OmpA-like transmembrane domain
1qjp opm.gif
Identifiers
Symbol OmpA_membrane
Pfam PF01389
Pfam clan CL0193
InterPro IPR000498
PROSITE PDOC00819
SCOP 1bxw
SUPERFAMILY 1bxw
TCDB 1.B.6
OPM superfamily 26
OPM protein 1qjp

OmpA-like transmembrane domain is an evolutionarily conserved domain of bacterial outer membrane proteins. This domain consists of an eight-stranded beta barrel.[1] OmpA is the predominant cell surface antigen in enterobacteria found in about 100,000 copies per cell.[2] The expression of OmpA is tightly regulated by a variety of mechanisms. One mechanism by which OmpA expression is regulated in Vibrio species is by an antisense non-coding RNA called VrrA.[3]

References[edit]

  1. ^ Pautsch A, Schulz GE (November 1998). "Structure of the outer membrane protein A transmembrane domain". Nat. Struct. Biol. 5 (11): 1013–7. doi:10.1038/2983. PMID 9808047. 
  2. ^ Smith SG, Mahon V, Lambert MA, Fagan RP (August 2007). "A molecular Swiss army knife: OmpA structure, function and expression". FEMS Microbiol. Lett. 273 (1): 1–11. doi:10.1111/j.1574-6968.2007.00778.x. PMID 17559395. 
  3. ^ Song T, Wai SN (July 2009). "A novel sRNA that modulates virulence and environmental fitness of Vibrio cholerae". RNA Biol 6 (3): 254–8. doi:10.4161/rna.6.3.8371. PMID 19411843. 


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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-like transmembrane domain Provide feedback

The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel [1]. This family includes some other distantly related outer membrane proteins with low scores.

Literature references

  1. Pautsch A, Schulz GE; , Nat Struct Biol 1998;5:1013-1017.: Structure of the outer membrane protein A transmembrane domain. PUBMED:9808047 EPMC:9808047


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000498

The ompA-like transmembrane domain is present in a number of different outer membrane proteins of several Gram-negative bacteria. Many of the proteins having this domain in the N-terminal also have the conserved bacterial outer membrane protein domain INTERPRO at the C terminus. The outer membrane protein A of Escherichia coli (OmpA), is one of the most studied proteins in this group [PUBMED:10554771]. It has a multifunctional role. OmpA is required for the action of colicins K and L and for the stabilisation of mating aggregates in conjugation. It also serves as a receptor for a number of T-even like phages and can act as a porin with low permeability that allows slow penetration of small solutes [PUBMED:1974149].

OmpA consists of a regular, extended eight-stranded beta-barrel and appears to be constructed like an inverse micelle with large water-filled cavities, but does not form a pore. The cavities seem to be highly conserved during evolution. The structure corroborates the concept that all outer membrane proteins consist of beta-barrels [PUBMED:9808047]. The beta-barrel membrane anchor appears to be the outer membrane equivalent of the single-chain alpha-helix anchor of the inner membrane.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Pfam Clan

This family is a member of clan MBB (CL0193), which has the following description:

This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.

The clan contains the following 54 members:

Ail_Lom Autotransporter Bac_surface_Ag Campylo_MOMP Channel_Tsx CopB DUF1302 DUF1597 DUF2320 DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3374 DUF3575 DUF4289 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL Phenol_MetA_deg Porin_1 Porin_2 Porin_4 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ

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...

View options

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
(13)
Full
(1301)
Representative proteomes NCBI
(2219)
Meta
(115)
RP15
(12)
RP35
(44)
RP55
(91)
RP75
(132)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(13)
Full
(1301)
Representative proteomes NCBI
(2219)
Meta
(115)
RP15
(12)
RP35
(44)
RP55
(91)
RP75
(132)
Alignment:
Format:
Order:
Sequence:
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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
(13)
Full
(1301)
Representative proteomes NCBI
(2219)
Meta
(115)
RP15
(12)
RP35
(44)
RP55
(91)
RP75
(132)
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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 13
Number in full: 1301
Average length of the domain: 165.60 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 47.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 183
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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_membrane domain has been found. There are 9 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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