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1  structure 4194  species 0  interactions 4687  sequences 17  architectures

Family: DNA_processg_A (PF02481)

Summary: DNA recombination-mediator protein A

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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.

DNA recombination-mediator protein A Provide feedback

The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation [1]. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation [2].

Literature references

  1. Smeets LC, Bijlsma JJ, Kuipers EJ, Vandenbroucke-Grauls CM, Kusters JG; , FEMS Immunol Med Microbiol 2000;27:99-102.: The dprA gene is required for natural transformation of Helicobacter pylori. PUBMED:10640603 EPMC:10640603

  2. Mortier-Barriere I, Velten M, Dupaigne P, Mirouze N, Pietrement O, McGovern S, Fichant G, Martin B, Noirot P, Le Cam E, Polard P, Claverys JP; , Cell. 2007;130:824-836.: A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. PUBMED:17803906 EPMC:17803906


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003488

The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In Helicobacter pylori, dprA is required for natural chromosomal and plasmid transformation [PUBMED:10640603]. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the Escherichia coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation [PUBMED:17803906].

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 DprA (CL0349), which has the following description:

Known family members of this superfamily are required for natural chromosomal and plasmid transformation. DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation [1]. Superfamily includes lysine_decarboxylases.

The clan contains the following 4 members:

DNA_processg_A DUF1273 Lysine_decarbox MoCo_carrier

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
(97)
Full
(4687)
Representative proteomes NCBI
(3571)
Meta
(633)
RP15
(340)
RP35
(676)
RP55
(868)
RP75
(1010)
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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
(97)
Full
(4687)
Representative proteomes NCBI
(3571)
Meta
(633)
RP15
(340)
RP35
(676)
RP55
(868)
RP75
(1010)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(97)
Full
(4687)
Representative proteomes NCBI
(3571)
Meta
(633)
RP15
(340)
RP35
(676)
RP55
(868)
RP75
(1010)
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_2252 (release 5.4)
Previous IDs: SMF;
Type: Family
Author: Mian N, Bateman A
Number in seed: 97
Number in full: 4687
Average length of the domain: 204.40 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 60.24 %

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 29.6 29.6
Trusted cut-off 29.7 29.7
Noise cut-off 29.5 29.5
Model length: 212
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 DNA_processg_A domain has been found. There are 1 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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