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0  structures 289  species 0  interactions 292  sequences 4  architectures

Family: DUF4937 (PF16291)

Summary: Domain of unknown function (DUF4937

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.

Domain of unknown function (DUF4937 Provide feedback

This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Bacillus species, such as Bacillus subtilis and Bacillus amyloliquefaciens. Several members are annotated as ydbC, but the specific function of this family is unknown.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032555

This domain can be found in a group of uncharacterised proteins around 120 residues in length and is found in bacteria.

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 Dim_A_B_barrel (CL0032), which has the following description:

This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel. The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases.

The clan contains the following 28 members:

ABM AsnC_trans_reg AsnC_trans_reg2 Chalcone_N Chlor_dismutase Cyclase_polyket Dabb Dehydratase_hem DUF1330 DUF1428 DUF3291 DUF4188 DUF4242 DUF4937 Dyp_perox EthD FtsX_ECD GYD HapK MIase MmlI NapD NIPSNAP rhaM SchA_CurD SOR YCII ydhR

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, the UniProtKB sequence database, 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
(12)
Full
(292)
Representative proteomes UniProt
(1114)
NCBI
(1606)
Meta
(0)
RP15
(23)
RP35
(145)
RP55
(297)
RP75
(478)
Jalview View  View  View  View  View  View  View  View   
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
(12)
Full
(292)
Representative proteomes UniProt
(1114)
NCBI
(1606)
Meta
(0)
RP15
(23)
RP35
(145)
RP55
(297)
RP75
(478)
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
(12)
Full
(292)
Representative proteomes UniProt
(1114)
NCBI
(1606)
Meta
(0)
RP15
(23)
RP35
(145)
RP55
(297)
RP75
(478)
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.

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 JCSG target MG14555A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Chang Y
Number in seed: 12
Number in full: 292
Average length of the domain: 78.30 aa
Average identity of full alignment: 62 %
Average coverage of the sequence by the domain: 40.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.3 28.3
Trusted cut-off 28.3 35.4
Noise cut-off 24.9 27.9
Model length: 89
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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Tree controls

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