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1  structure 258  species 0  interactions 265  sequences 1  architecture

Family: 2H-phosphodiest (PF08975)

Summary: Domain of unknown function (DUF1868)

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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.

Domain of unknown function (DUF1868) Provide feedback

This group of 2H-phosphodiesterases comprises a single family typified by the protein mlr3352 from M.loti. Members are also present in various alpha-proteobacteria, Synechocystis, Streptococcus and Chilo iridescent virus. The presence of a member of this predominantly bacterial group in a large eukaryotic DNA virus represents a potential case of horizontal transfer from a bacterial source into a virus. Several proteins of bacterial origin have been noticed in the insect viruses (L.M.Iyer, E.V.Koonin and L.Aravind, unpublished observations and these appear to have been acquired from endo-symbiotic or parasitic bacteria that share the same host cells with the viruses. Presence of 2H proteins in the proteomes of large DNA viruses (e.g. T4 57B protein and the Fowl-pox virus FPV025) may point to some role for these proteins in regulating the viral tRNA metabolism. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family.

Literature references

  1. Mazumder R, Iyer LM, Vasudevan S, Aravind L; , Nucleic Acids Res 2002;30:5229-5243.: Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. PUBMED:12466548 EPMC:12466548


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015069

This presumed domain is functionally uncharacterised.

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 2H (CL0247), which contains the following 9 members:

2_5_RNA_ligase2 2H-phosphodiest AKAP7_NLS CNPase Corona_NS2A CPDase DUF1045 HVSL LigT_PEase

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
(13)
Full
(265)
Representative proteomes NCBI
(106)
Meta
(81)
RP15
(5)
RP35
(17)
RP55
(22)
RP75
(37)
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PP/heatmap 1 View  View  View  View  View     
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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
(13)
Full
(265)
Representative proteomes NCBI
(106)
Meta
(81)
RP15
(5)
RP35
(17)
RP55
(22)
RP75
(37)
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
(13)
Full
(265)
Representative proteomes NCBI
(106)
Meta
(81)
RP15
(5)
RP35
(17)
RP55
(22)
RP75
(37)
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: pdb_2fsq
Previous IDs: DUF1868;
Type: Domain
Author: Mistry J, Sammut SJ
Number in seed: 13
Number in full: 265
Average length of the domain: 117.50 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 51.47 %

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 21.0 21.0
Trusted cut-off 21.3 21.1
Noise cut-off 20.7 20.9
Model length: 118
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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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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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 2H-phosphodiest domain has been found. There are 1 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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