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.
321  structures 1344  species 0  interactions 3357  sequences 94  architectures

Family: DRMBL (PF07522)

Summary: DNA repair metallo-beta-lactamase

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.

DNA repair metallo-beta-lactamase Provide feedback

The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in PF00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair [1].

Literature references

  1. Callebaut I, Moshous D, Mornon JP, de Villartay JP; , Nucleic Acids Res 2002;30:3592-3601.: Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. PUBMED:12177301 EPMC:12177301


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011084

The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair [ PUBMED:12177301 ].

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 RMMBL_DRMBL (CL0398), which has the following description:

This clan contains the fifth motif found in RNA and DNA metabolising metallo-beta-lactamases. The fifth motif appears to be specific to function [1].

The clan contains the following 2 members:

DRMBL RMMBL

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
(29)
Full
(3357)
Representative proteomes UniProt
(5486)
RP15
(522)
RP35
(1492)
RP55
(2683)
RP75
(3604)
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
(29)
Full
(3357)
Representative proteomes UniProt
(5486)
RP15
(522)
RP35
(1492)
RP55
(2683)
RP75
(3604)
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
(29)
Full
(3357)
Representative proteomes UniProt
(5486)
RP15
(522)
RP35
(1492)
RP55
(2683)
RP75
(3604)
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: Mannual
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 29
Number in full: 3357
Average length of the domain: 106.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 14.65 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 116
Family (HMM) version: 16
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 DRMBL domain has been found. There are 321 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
A0A0P0XNK3 View 3D Structure Click here
A0A0R0EKG2 View 3D Structure Click here
A0A1D6EI92 View 3D Structure Click here
A0A1D6LQM1 View 3D Structure Click here
A0A1D6M1T7 View 3D Structure Click here
A0A1D6M6C0 View 3D Structure Click here
A0A1D6NFC7 View 3D Structure Click here
A0A1D8PCQ2 View 3D Structure Click here
A0A1X7YGN1 View 3D Structure Click here
A4IA93 View 3D Structure Click here
B0V2S2 View 3D Structure Click here
C0PFV3 View 3D Structure Click here
D3Z924 View 3D Structure Click here
E7F457 View 3D Structure Click here
F4HPZ9 View 3D Structure Click here
F4IDZ7 View 3D Structure Click here
I1K8I7 View 3D Structure Click here
I1KBJ2 View 3D Structure Click here
I1LRV5 View 3D Structure Click here
I1ML74 View 3D Structure Click here
K7MVF2 View 3D Structure Click here
K7TT02 View 3D Structure Click here
K7TXP1 View 3D Structure Click here
O64649 View 3D Structure Click here
P30620 View 3D Structure Click here
Q10264 View 3D Structure Click here
Q38961 View 3D Structure Click here
Q4DNU5 View 3D Structure Click here
Q4KLY6 View 3D Structure Click here
Q5RGE5 View 3D Structure Click here
Q5XIX3 View 3D Structure Click here
Q6PJP8 View 3D Structure Click here
Q6ZD68 View 3D Structure Click here
Q7XV88 View 3D Structure Click here
Q86KS1 View 3D Structure Click here
Q8C7W7 View 3D Structure Click here
Q8IK95 View 3D Structure Click here
Q8K4J0 View 3D Structure Click here
Q8RZQ7 View 3D Structure Click here
Q8T3E0 View 3D Structure Click here
Q96SD1 View 3D Structure Click here
Q9H816 View 3D Structure Click here
Q9JIC3 View 3D Structure Click here
Q9VND2 View 3D Structure Click here