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48  structures 921  species 1  interaction 1481  sequences 15  architectures

Family: Dabb (PF07876)

Summary: Stress responsive A/B Barrel Domain

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Stress responsive A/B Barrel Domain Provide feedback

The function of this family is unknown, but it is upregulated in response to salt stress in Populus balsamifera ([1]). It is also found at the C-terminus of an fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (Q9ZA13; [2]). Q93NG5 is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The structure of one has been solved (Q9LUV2) and the domain forms an a/b barrel dimer ([3]). Although there is a clear duplication within the domain it is not obviously detectable in the sequence.

Literature references

  1. Gu R, Fonseca S, Puskas LG, Hackler L Jr, Zvara A, Dudits D, Pais MS; , Tree Physiol 2004;24:265-276.: Transcript identification and profiling during salt stress and recovery of Populus euphratica. PUBMED:14704136 EPMC:14704136

  2. Hayashi NR, Terazono K, Kodama T, Igarashi Y; , Biosci Biotechnol Biochem 2000;64:61-71.: Structure of ribulose 1,5-bisphosphate carboxylase/oxygenase gene cluster from a thermophilic hydrogen-oxidizing bacterium, Hydrogenophilus thermoluteolus, and phylogeny of the fructose 1,6-bisphosphate aldolase encoded by cbbA in the cluster. PUBMED:10705449 EPMC:10705449

  3. Lytle BL, Peterson FC, Kjer KL, Frederick RO, Zhao Q, Thao S, Bingman C, Johnson KA, Phillips GN Jr, Volkman BF; , J Biomol NMR 2004;28:397-400.: Structure of the hypothetical protein At3g17210 from Arabidopsis thaliana. PUBMED:14872131 EPMC:14872131


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013097

The stress-response A/B barrel domain is found in a class of stress-response proteins in plants. It is also found in some bacterial fructose-bisphosphate aldolase such as at the C terminus of a fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (SWISSPROT) [PUBMED:10705449]. SWISSPROT is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine.

The stress-response A/B barrel domain forms a very stable dimer. This dimer belongs to the superfamily of dimeric alpha+beta barrels in which the two beta-sheets form a beta-barrel. The two molecules in the dimer are related by a 2-fold axis parallel to helix H1 and beta-strands B3 and B4. C-terminal residues extending from the beta4 strand of each monomer wrap around and connect with the beta2 strand and alpha1 helix of the opposing monomer to form the dimer interface [PUBMED:15364906, PUBMED:15213437, PUBMED:15371455].The outer surface of the beta-sheets of the two molecules forms a beta-barrel-like structure defining a central pore.

The function of the stress-response A/B barrel domain is unknown [PUBMED:15364906, PUBMED:15213437, PUBMED:15371455], but it is upregulated in response to salt stress in Populus balsamifera (balsam poplar) [PUBMED:14704136].

Some proteins known to contain a stress response A/B barrel domain are listed below:

- Arabidopsis thaliana At3g17210

- Arabidopsis thaliana At5g22580

-Populus tremula stable protein 1 (SP-1)(Populus species), a thermostable stress-responsive protein.

- Pseudomonas hydrogenothermophila fructose 1,6-bisphosphate aldolase (cbbA).

The structure of one of these proteins has been solved (SWISSPROT) and the domain forms an alpha-beta barrel dimer [PUBMED:14872131].

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.

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(51)
Full
(1481)
Representative proteomes NCBI
(1398)
Meta
(234)
RP15
(173)
RP35
(439)
RP55
(571)
RP75
(686)
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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
(51)
Full
(1481)
Representative proteomes NCBI
(1398)
Meta
(234)
RP15
(173)
RP35
(439)
RP55
(571)
RP75
(686)
Alignment:
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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
(51)
Full
(1481)
Representative proteomes NCBI
(1398)
Meta
(234)
RP15
(173)
RP35
(439)
RP55
(571)
RP75
(686)
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: Yeats C
Previous IDs: none
Type: Domain
Author: Yeats C
Number in seed: 51
Number in full: 1481
Average length of the domain: 96.20 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 80.22 %

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 21.2 21.2
Trusted cut-off 21.4 21.2
Noise cut-off 21.0 21.1
Model length: 97
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Dabb

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 Dabb domain has been found. There are 48 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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