!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at legacy.pfam.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

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.
24  structures 713  species 0  interactions 1965  sequences 31  architectures

Family: UMPH-1 (PF05822)

Summary: Pyrimidine 5'-nucleotidase (UMPH-1)

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.

Pyrimidine 5'-nucleotidase (UMPH-1) Provide feedback

This family consists of several eukaryotic pyrimidine 5'-nucleotidase proteins. P5'N-1, also known as uridine monophosphate hydrolase-1 (UMPH-1), is a member of a large functional group of enzymes, characterised by the ability to dephosphorylate nucleic acids. P5'N-1 catalyses the dephosphorylation of pyrimidine nucleoside monophosphates to the corresponding nucleosides. Deficiencies in this proteins function can lead to several different disorders in humans [1].

Literature references

  1. Rees DC, Duley JA, Marinaki AM; , Br J Haematol 2003;120:375-383.: Pyrimidine 5' nucleotidase deficiency. PUBMED:12580951 EPMC:12580951


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006434

This family is a small group of metazoan sequences with sequences from Arabidopsis thaliana (Mouse-ear cress) and rice. The sequences represent pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the Homo sapiens (Human) homologue [ PUBMED:10942414 ]. The structure of mouse sequence has been reported [ PUBMED:16672222 ]. This group of sequences was originally found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs [ PUBMED:7966317 ] are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.

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 HAD (CL0137), which has the following description:

This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [1].

The clan contains the following 25 members:

5_nucleotid Acid_phosphat_B Acid_PPase APP1_cat Cation_ATPase DHH DUF2608 DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like LNS2 NIF NT5C PGP_phosphatase PhoLip_ATPase_C PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1

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 and the UniProtKB 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
(9)
Full
(1965)
Representative proteomes UniProt
(3389)
RP15
(386)
RP35
(820)
RP55
(1571)
RP75
(2020)
Jalview 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
(9)
Full
(1965)
Representative proteomes UniProt
(3389)
RP15
(386)
RP35
(820)
RP55
(1571)
RP75
(2020)
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
(9)
Full
(1965)
Representative proteomes UniProt
(3389)
RP15
(386)
RP35
(820)
RP55
(1571)
RP75
(2020)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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_7840 (release 8.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 9
Number in full: 1965
Average length of the domain: 212.2 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 74.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.7 23.7
Trusted cut-off 23.7 23.7
Noise cut-off 23.6 23.6
Model length: 246
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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 UMPH-1 domain has been found. There are 24 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 sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044R1X9 View 3D Structure Click here
A0A044R268 View 3D Structure Click here
A0A077Z6Y3 View 3D Structure Click here
A0A0J9Y5H4 View 3D Structure Click here
A0A0K0DUX1 View 3D Structure Click here
A0A0K0E1G9 View 3D Structure Click here
A0A0K0ECN8 View 3D Structure Click here
A0A0N4UAL3 View 3D Structure Click here
A0A0R0HVX0 View 3D Structure Click here
A0A158Q480 View 3D Structure Click here
A0A1D6GLD3 View 3D Structure Click here
A0A3P7G899 View 3D Structure Click here
A0A3Q0KGL8 View 3D Structure Click here
A0A3Q0KJH9 View 3D Structure Click here
A0A5K4EJM6 View 3D Structure Click here
A0A5K4FBW1 View 3D Structure Click here
A0A5S6PRW7 View 3D Structure Click here
B2GUX5 View 3D Structure Click here
F4ITW1 View 3D Structure Click here
I1NHU7 View 3D Structure Click here
J9F1C0 View 3D Structure Click here
K7LIN1 View 3D Structure Click here
Q09315 View 3D Structure Click here
Q3UFY7 View 3D Structure Click here
Q5ZID6 View 3D Structure Click here
Q5ZKF6 View 3D Structure Click here
Q60DI6 View 3D Structure Click here
Q6AYP7 View 3D Structure Click here
Q7SYN4 View 3D Structure Click here
Q95ZJ9 View 3D Structure Click here
Q969T7 View 3D Structure Click here
Q9D020 View 3D Structure Click here
Q9H0P0 View 3D Structure Click here
Q9W197 View 3D Structure Click here