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0  structures 60  species 0  interactions 722  sequences 8  architectures

Family: PDDEXK_6 (PF04720)

Summary: PDDEXK-like family of unknown function

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.

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.

PDDEXK-like family of unknown function Provide feedback

PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix [1]. The family is not in general fused with any other domains, so its function cannot be predicted [2].

Literature references

  1. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K; , BMC Struct Biol. 2007;7:40.: Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. PUBMED:17584917 EPMC:17584917

  2. Jorgensen RA, Dorantes-Acosta AE;, Front Plant Sci. 2012;3:191.: Conserved Peptide Upstream Open Reading Frames are Associated with Regulatory Genes in Angiosperms. PUBMED:22936940 EPMC:22936940


This tab holds annotation information from the InterPro database.

InterPro entry IPR006502

PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix [PUBMED:17584917]. The family is not in general fused with any other domains, so its function cannot be predicted [PUBMED:22936940].

This family of uncharacterised plant proteins are defined by a region found toward the C terminus. This region is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.

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 (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...

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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
(104)
Full
(722)
Representative proteomes UniProt
(933)
NCBI
(1153)
Meta
(2)
RP15
(93)
RP35
(346)
RP55
(622)
RP75
(712)
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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
(104)
Full
(722)
Representative proteomes UniProt
(933)
NCBI
(1153)
Meta
(2)
RP15
(93)
RP35
(346)
RP55
(622)
RP75
(712)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(104)
Full
(722)
Representative proteomes UniProt
(933)
NCBI
(1153)
Meta
(2)
RP15
(93)
RP35
(346)
RP55
(622)
RP75
(712)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Pfam-B_4111 (release 7.5)
Previous IDs: DUF506;
Type: Family
Author: Waterfield DI, Finn RD
Number in seed: 104
Number in full: 722
Average length of the domain: 193.90 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 64.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 27.1 25.1
Noise cut-off 24.6 24.0
Model length: 209
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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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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