Summary: Taq polymerase, exonuclease
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Taq polymerase, exonuclease Provide feedback
Members of this family are found in prokaryotic Taq DNA polymerase, where they assume a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase [1].
Literature references
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Li Y, Mitaxov V, Waksman G; , Proc Natl Acad Sci U S A. 1999;96:9491-9496.: Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. PUBMED:10449720 EPMC:10449720
External database links
SCOP: | 1qtm |
This tab holds annotation information from the InterPro database.
InterPro entry IPR015361
This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase [PUBMED:10449720].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | DNA-directed DNA polymerase activity (GO:0003887) |
nucleoside binding (GO:0001882) | |
Biological process | DNA repair (GO:0006281) |
DNA replication (GO:0006260) |
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 RNase_H (CL0219), which has the following description:
This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H.
The clan contains the following 61 members:
Arena_ncap_C CAF1 DDE_1 DDE_2 DDE_3 DDE_5 DDE_Tnp_1 DDE_Tnp_1_2 DDE_Tnp_1_3 DDE_Tnp_1_4 DDE_Tnp_1_5 DDE_Tnp_1_6 DDE_Tnp_1_7 DDE_Tnp_2 DDE_Tnp_4 DDE_Tnp_IS1 DDE_Tnp_IS1595 DDE_Tnp_IS240 DDE_Tnp_IS66 DDE_Tnp_ISAZ013 DDE_Tnp_ISL3 Dimer_Tnp_Tn5 DNA_pol_A_exo1 DNA_pol_B_exo1 DNA_pol_B_exo2 DNA_pol_P_Exo DUF1258 DUF2779 DUF3882 DUF4152 DUF5051 KDZ Maelstrom MULE NurA OrfB_IS605 Piwi Plant_tran Plavaka Pox_A22 RNase_H RNase_H_2 RNase_HII RNase_T RNaseH_like RT_RNaseH RT_RNaseH_2 RuvC RuvC_1 rve rve_2 rve_3 RVT_3 Taq-exonuc Terminase_3C Terminase_6C Transposase_1 Transposase_21 Transposase_mut UPF0236 Ydc2-catalytAlignments
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...
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 (31) |
Representative proteomes | UniProt (72) |
NCBI (129) |
Meta (0) |
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RP15 (3) |
RP35 (15) |
RP55 (35) |
RP75 (44) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (31) |
Representative proteomes | UniProt (72) |
NCBI (129) |
Meta (0) |
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RP15 (3) |
RP35 (15) |
RP55 (35) |
RP75 (44) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | pdb_1qtm |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Sammut SJ |
Number in seed: | 9 |
Number in full: | 31 |
Average length of the domain: | 122.40 aa |
Average identity of full alignment: | 38 % |
Average coverage of the sequence by the domain: | 16.30 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 129 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
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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Interactions
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 Taq-exonuc domain has been found. There are 58 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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