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9  structures 1074  species 0  interactions 1696  sequences 5  architectures

Family: DmpG_comm (PF07836)

Summary: DmpG-like communication 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 "DmpG-like communication domain". More...

DmpG-like communication domain Edit Wikipedia article

DmpG-like communication domain
PDB 1nvm EBI.jpg
crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate
Identifiers
SymbolDmpG_comm
PfamPF07836
InterProIPR012425
SCOP21nvm / SCOPe / SUPFAM

In molecular biology, the DmpG-like communication domain is a protein domain found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain.[1] The communication domain is thought to play an important role in the heterodimerisation of the enzyme.[1]

This domain heterodimerises with acetaldehyde dehydrogenases to form a bifunctional aldolase-dehydrogenase.[1]

References

  1. ^ a b c Manjasetty BA, Powlowski J, Vrielink A (2003). "Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate". Proc. Natl. Acad. Sci. U.S.A. 100 (12): 6992–7. doi:10.1073/pnas.1236794100. PMC 165818. PMID 12764229. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR012425

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.

DmpG-like communication domain Provide feedback

This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain [1]. The communication domain is thought to play an important role in the heterodimerisation of the enzyme [1].

Literature references

  1. Manjasetty BA, Powlowski J, Vrielink A; , Proc Natl Acad Sci U S A 2003;100:6992-6997.: Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. PUBMED:12764229 EPMC:12764229


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012425

This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain [ PUBMED:12764229 ]. The communication domain is thought to play an important role in the heterodimerisation of the enzyme [ PUBMED:12764229 ].

Members of this entry heterodimerise with members of INTERPRO to form a bifunctional aldolase-dehydrogenase [ PUBMED:12764229 ].

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 Post-HMGL (CL0597), which has the following description:

The clan contains the following 2 members:

DmpG_comm PYC_OADA

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(55)
Full
(1696)
Representative proteomes UniProt
(7800)
RP15
(138)
RP35
(669)
RP55
(1811)
RP75
(3424)
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HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(55)
Full
(1696)
Representative proteomes UniProt
(7800)
RP15
(138)
RP35
(669)
RP55
(1811)
RP75
(3424)
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
(55)
Full
(1696)
Representative proteomes UniProt
(7800)
RP15
(138)
RP35
(669)
RP55
(1811)
RP75
(3424)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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_1675 (release 14.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Fenech M
Number in seed: 55
Number in full: 1696
Average length of the domain: 62.6 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 18.58 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.2 27.3
Noise cut-off 26.5 26.7
Model length: 63
Family (HMM) version: 14
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 DmpG_comm 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3GU24 View 3D Structure Click here
A0QZU2 View 3D Structure Click here
A0R4S6 View 3D Structure Click here
A1K6L9 View 3D Structure Click here
A1K6Y4 View 3D Structure Click here
A1K893 View 3D Structure Click here
A1SH77 View 3D Structure Click here
A1SIM3 View 3D Structure Click here
A1T2N6 View 3D Structure Click here
A1TDB7 View 3D Structure Click here
A1TFQ5 View 3D Structure Click here
A1UM80 View 3D Structure Click here
A1UQA1 View 3D Structure Click here
A1VUV1 View 3D Structure Click here
A1W2K3 View 3D Structure Click here
A1WLL2 View 3D Structure Click here
A2SI33 View 3D Structure Click here
A2SL35 View 3D Structure Click here
A4XAK7 View 3D Structure Click here
A4XDT6 View 3D Structure Click here
A4XF35 View 3D Structure Click here
A5D523 View 3D Structure Click here
A5UWE6 View 3D Structure Click here
A5V6T8 View 3D Structure Click here
A5V856 View 3D Structure Click here
A5VGU4 View 3D Structure Click here
A6TAC4 View 3D Structure Click here
A7IDU6 View 3D Structure Click here
A8H4E9 View 3D Structure Click here
A8LAA1 View 3D Structure Click here
A8LEP8 View 3D Structure Click here
A9W9U3 View 3D Structure Click here
B1KJK9 View 3D Structure Click here
B1Y2E5 View 3D Structure Click here
B2HGH1 View 3D Structure Click here
B2HI25 View 3D Structure Click here
B2JLM6 View 3D Structure Click here
B2JQW0 View 3D Structure Click here
B2UJF1 View 3D Structure Click here
B8ESV2 View 3D Structure Click here