Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
2  structures 1995  species 0  interactions 3851  sequences 6  architectures

Family: DUF3816 (PF12822)

Summary: Protein of unknown function (DUF3816)

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

Protein of unknown function (DUF3816) Provide feedback

This family of proteins is functionally uncharacterised but are likely to be membrane transporters. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 177 and 208 amino acids in length. A subset of this family is associated with the TM1506 proteins. In this context, transport through the channel is predicted to be regulated by the TM1506 protein by either regulating redox potential or modification of substrates [1]

Literature references

  1. Iyer LM, Zhang D, Rogozin IB, Aravind L;, Nucleic Acids Res. 2011; [Epub ahead of print]: Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PUBMED:21890906 EPMC:21890906


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024529

Energy-coupling factor (ECF) transporters consist of a substrate-specific component (known as the S component), and an energy-coupling module [PUBMED:18931129]. The substrate-binding component is a small integral membrane protein which captures specific substrates and forms an active transporter in the presence of the energy-coupling AT module. The energy coupling module is composed of an ATPase typical of the ATP binding cassette (ABC) superfamily (A component) and a characteristic transmembrane protein (T component). Unlike the ABC transporters, an energy coupling module can be shared between multiple different substrate-binding components.

This entry represents the substrate-specific component from a number of different ECF transporters.

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan Gx_transp (CL0315), which has the following description:

This superfamily includes a wide range of transporters that contain many conserved glycine residues in the presumed transmembrane regions.

The clan contains the following 12 members:

5TM-5TMR_LYT Bac_export_3 BioY CbiM DUF2232 DUF3816 ECF-ribofla_trS Hpre_diP_synt_I MreD QueT Thia_YuaJ ThiW

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
(172)
Full
(3851)
Representative proteomes NCBI
(3039)
Meta
(57)
RP15
(216)
RP35
(361)
RP55
(451)
RP75
(522)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(172)
Full
(3851)
Representative proteomes NCBI
(3039)
Meta
(57)
RP15
(216)
RP35
(361)
RP55
(451)
RP75
(522)
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
(172)
Full
(3851)
Representative proteomes NCBI
(3039)
Meta
(57)
RP15
(216)
RP35
(361)
RP55
(451)
RP75
(522)
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.

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: Jackhmmer:Q188H8
Previous IDs: none
Type: Family
Author: Bateman A, Iyer LM
Number in seed: 172
Number in full: 3851
Average length of the domain: 168.30 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 85.15 %

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 30.0 30.0
Trusted cut-off 30.0 30.0
Noise cut-off 29.9 29.9
Model length: 172
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 DUF3816 domain has been found. There are 2 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.

Loading structure mapping...