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19  structures 100  species 3  interactions 198  sequences 2  architectures

Family: DUF1297 (PF06973)

Summary: Domain of unknown function (DUF1297)

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 (DUF1297) Provide feedback

This family represents the C-terminus (approximately 200 residues) of a number of archaeal proteins of unknown function. One member is annotated as being a possible carboligase enzyme.

This tab holds annotation information from the InterPro database.

InterPro entry IPR009720

The last two steps of de novo purine biosynthesis are:

  • i) conversion of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR)
  • ii) conversion of FAICAR to inosine5'-monophopsphate (IMP)
In bacteria and eukaryotes, these steps are catalysed by the well-characterised bifunctional enzyme PurH [PUBMED:11323713]. Archaea do not appear to posses PurH, however, and perform these reactions by a different mechanism [PUBMED:9150241]. In archaea, step i) is catalysed by the well-conserved PurP protein, while step ii) is catalysed by the PurO enzyme in some (though not all) species [PUBMED:15623504, PUBMED:11844782].

This entry represents the C-terminal domain of PurP, which is homologous to the ATP-GRASP fold and thus may be involved in ATP-binding. It is almost always found in association with INTERPRO.

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 ATP-grasp (CL0179), which has the following description:

The ATP-grasp domain is found in a wide variety of carboxylate-amine/thiol ligases [1]. It is composed of two subdomains, with ATP being bound in the cleft between the two.

The clan contains the following 21 members:

ATP-grasp ATP-grasp_2 ATP-grasp_3 ATP-grasp_4 ATP-grasp_5 ATPgrasp_ST ATPgrasp_Ter ATPgrasp_TupA ATPgrasp_YheCD CP_ATPgrasp_1 CP_ATPgrasp_2 CPSase_L_D2 Dala_Dala_lig_C DUF1297 GARS_A GSH-S_ATP GSP_synth Ins134_P3_kin RimK Synapsin_C TTL

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
(61)
Full
(198)
Representative proteomes UniProt
(548)
NCBI
(535)
Meta
(129)
RP15
(78)
RP35
(113)
RP55
(186)
RP75
(286)
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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
(61)
Full
(198)
Representative proteomes UniProt
(548)
NCBI
(535)
Meta
(129)
RP15
(78)
RP35
(113)
RP55
(186)
RP75
(286)
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
(61)
Full
(198)
Representative proteomes UniProt
(548)
NCBI
(535)
Meta
(129)
RP15
(78)
RP35
(113)
RP55
(186)
RP75
(286)
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_3819 (release 10.0)
Previous IDs: none
Type: Domain
Author: Vella Briffa B
Number in seed: 61
Number in full: 198
Average length of the domain: 182.50 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 52.68 %

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 23.8 23.8
Trusted cut-off 24.3 25.5
Noise cut-off 21.9 22.9
Model length: 188
Family (HMM) version: 10
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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Interactions

There are 3 interactions for this family. More...

DUF1297 DUF1246 DUF1246

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 DUF1297 domain has been found. There are 19 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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