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690  structures 2348  species 0  interactions 4527  sequences 97  architectures

Family: DNA_pol_B_thumb (PF14791)

Summary: DNA polymerase beta thumb

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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 polymerase beta thumb Provide feedback

The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain [1].

Literature references

  1. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J;, Science. 1994;264:1930-1935.: Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. PUBMED:7516581 EPMC:7516581


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR029398

The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain [ PUBMED:7516581 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(341)
Full
(4527)
Representative proteomes UniProt
(14180)
RP15
(756)
RP35
(1962)
RP55
(3707)
RP75
(5362)
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
(341)
Full
(4527)
Representative proteomes UniProt
(14180)
RP15
(756)
RP35
(1962)
RP55
(3707)
RP75
(5362)
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
(341)
Full
(4527)
Representative proteomes UniProt
(14180)
RP15
(756)
RP35
(1962)
RP55
(3707)
RP75
(5362)
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: CATH:2van_A_03
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 341
Number in full: 4527
Average length of the domain: 68.80 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 12.41 %

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 25.0 25.0
Trusted cut-off 25.1 25.0
Noise cut-off 24.9 24.9
Model length: 68
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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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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 DNA_pol_B_thumb domain has been found. There are 690 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
A0A1D6NRF0 View 3D Structure Click here
A4HTM9 View 3D Structure Click here
A4HTN0 View 3D Structure Click here
B3DKA1 View 3D Structure Click here
B8JIE9 View 3D Structure Click here
E9PT58 View 3D Structure Click here
I1JCZ1 View 3D Structure Click here
O02789 View 3D Structure Click here
P04053 View 3D Structure Click here
P06526 View 3D Structure Click here
P06746 View 3D Structure Click here
P06766 View 3D Structure Click here
P09838 View 3D Structure Click here
P25615 View 3D Structure Click here
P36195 View 3D Structure Click here
P94544 View 3D Structure Click here
Q09693 View 3D Structure Click here
Q1ZXF2 View 3D Structure Click here
Q27958 View 3D Structure Click here
Q2FZD4 View 3D Structure Click here
Q4CUC9 View 3D Structure Click here
Q4DD98 View 3D Structure Click here
Q4DH94 View 3D Structure Click here
Q4DH95 View 3D Structure Click here
Q4E023 View 3D Structure Click here
Q4E024 View 3D Structure Click here
Q4R380 View 3D Structure Click here
Q5IBN3 View 3D Structure Click here
Q5RKI3 View 3D Structure Click here
Q66HH0 View 3D Structure Click here
Q67VC8 View 3D Structure Click here
Q6DRD3 View 3D Structure Click here
Q8K409 View 3D Structure Click here
Q9FNY4 View 3D Structure Click here
Q9JIW4 View 3D Structure Click here
Q9NP87 View 3D Structure Click here
Q9QXE2 View 3D Structure Click here
Q9UGP5 View 3D Structure Click here