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1  structure 1395  species 0  interactions 4120  sequences 54  architectures

Family: AMP_deaminase (PF19326)

Summary: AMP deaminase

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.

AMP deaminase Provide feedback

No Pfam abstract.

Literature references

  1. Han BW, Bingman CA, Mahnke DK, Bannen RM, Bednarek SY, Sabina RL, Phillips GN Jr;, J Biol Chem. 2006;281:14939-14947.: Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1). PUBMED:16543243 EPMC:16543243


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 Amidohydrolase (CL0034), which has the following description:

This family includes a large family of metal dependent amidohydrolase enzymes [1].

The clan contains the following 17 members:

A_deaminase Amidohydro_1 Amidohydro_2 Amidohydro_3 AMP_deaminase CpsB_CapC DHOase DUF3604 DUF6282 Peptidase_M19 PHP PHP_C PTE RNase_P_p30 TatD_DNase Urease_alpha UxaC

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
(6)
Full
(4120)
Representative proteomes UniProt
(8135)
RP15
(661)
RP35
(1728)
RP55
(3382)
RP75
(4530)
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
(6)
Full
(4120)
Representative proteomes UniProt
(8135)
RP15
(661)
RP35
(1728)
RP55
(3382)
RP75
(4530)
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
(6)
Full
(4120)
Representative proteomes UniProt
(8135)
RP15
(661)
RP35
(1728)
RP55
(3382)
RP75
(4530)
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

This family is new in this Pfam release.

Seed source: PF00962
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 6
Number in full: 4120
Average length of the domain: 530.60 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 75.88 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 633
Family (HMM) version: 1
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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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 AMP_deaminase 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 sequence.

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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
A0A0J9YJL9 View 3D Structure Click here
A0A0P0WL35 View 3D Structure Click here
A0A0R0GJI1 View 3D Structure Click here
A0A0R0GRB6 View 3D Structure Click here
A0A0R0HC27 View 3D Structure Click here
A0A1D6IP63 View 3D Structure Click here
A0A1D6IP63 View 3D Structure Click here
A0A1D6M2L4 View 3D Structure Click here
A0A1D6M2L4 View 3D Structure Click here
A0A2C9C377 View 3D Structure Click here
A0A2R8PWK1 View 3D Structure Click here
A0A2R8PWK1 View 3D Structure Click here
A4HS23 View 3D Structure Click here
A4HS23 View 3D Structure Click here
A4HS23 View 3D Structure Click here
A4HVM6 View 3D Structure Click here
A4HVM6 View 3D Structure Click here
A4I876 View 3D Structure Click here
A4I876 View 3D Structure Click here
A4I876 View 3D Structure Click here
A4IC17 View 3D Structure Click here
A4IC17 View 3D Structure Click here
B8JIS9 View 3D Structure Click here
I1JLC7 View 3D Structure Click here
I1KXP5 View 3D Structure Click here
K7K3C2 View 3D Structure Click here
K7MRP9 View 3D Structure Click here
O08739 View 3D Structure Click here
O09178 View 3D Structure Click here
O80452 View 3D Structure Click here
P10759 View 3D Structure Click here
P15274 View 3D Structure Click here
P23109 View 3D Structure Click here
P38150 View 3D Structure Click here
P40361 View 3D Structure Click here
P40361 View 3D Structure Click here
P50998 View 3D Structure Click here
Q01432 View 3D Structure Click here
Q01433 View 3D Structure Click here
Q02356 View 3D Structure Click here
Q1LYD7 View 3D Structure Click here
Q3V1D3 View 3D Structure Click here
Q4CL49 View 3D Structure Click here
Q4CL49 View 3D Structure Click here
Q4CLL4 View 3D Structure Click here
Q4CLX2 View 3D Structure Click here
Q4CLX2 View 3D Structure Click here
Q4CS44 View 3D Structure Click here
Q4D5V1 View 3D Structure Click here
Q4D9D3 View 3D Structure Click here
Q4DAJ9 View 3D Structure Click here
Q4DAJ9 View 3D Structure Click here
Q4DII0 View 3D Structure Click here
Q4DII0 View 3D Structure Click here
Q4DII0 View 3D Structure Click here
Q4DMR1 View 3D Structure Click here
Q4DWY4 View 3D Structure Click here
Q4DWY4 View 3D Structure Click here
Q4E4G2 View 3D Structure Click here
Q4E4G2 View 3D Structure Click here
Q54DD0 View 3D Structure Click here
Q5AHA6 View 3D Structure Click here
Q6P3G5 View 3D Structure Click here
Q84NP7 View 3D Structure Click here
Q8IE53 View 3D Structure Click here
Q9DBT5 View 3D Structure Click here
X2JEY5 View 3D Structure Click here