Summary: RNA repair pathway DNA polymerase beta family
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RNA repair pathway DNA polymerase beta family Provide feedback
Family of the DNA polymerase beta superfamily, with closest affinities to the Minimal Nucleotide Transferase clade (MNT). Observed in diverse RNA repair genome contexts centered on both RtcB and Rnl-type (ATP-grasp fold) repair ligases [1]. Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Literature references
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Burroughs AM, Aravind L;, Nucleic Acids Res. 2016;44:8525-8555.: RNA damage in biological conflicts and the diversity of responding RNA repair systems. PUBMED:27536007 EPMC:27536007
Internal database links
SCOOP: | NTP_transf_2 Polbeta |
This tab holds annotation information from the InterPro database.
InterPro entry IPR018775
This entry represents a group of proteins that belong to the DNA polymerase beta superfamily, with closest affinities to the Minimal Nucleotide Transferase clade (MNT). They are found in diverse RNA repair genome contexts centred on both RtcB and Rnl-type (ATP-grasp fold) repair ligases [PUBMED:27536007]. Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
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 NTP_transf (CL0260), which has the following description:
This clan contains a diverse set of nucleotidyltransferase enzymes.
The clan contains the following 31 members:
AbiEii Adenyl_cycl_N Adenyl_transf Aminoglyc_resit DNA_pol3_alpha DNA_pol_B_palm DUF2204 DUF294 DUF4269 DZF GlnE GrpB LicD MdcG Nrap Nrap_D4 NTF-like NTP_transf_2 NTP_transf_5 NTP_transf_6 NTP_transf_7 NTP_transf_8 Polbeta PolyA_pol Pox_polyA_pol RelA_SpoT RlaP RsfS SMODS Tam41_Mmp37 TUTaseAlignments
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...
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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 (25) |
Full (1978) |
Representative proteomes | UniProt (7976) |
NCBI (12073) |
Meta (31) |
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RP15 (387) |
RP35 (953) |
RP55 (1986) |
RP75 (3470) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (25) |
Full (1978) |
Representative proteomes | UniProt (7976) |
NCBI (12073) |
Meta (31) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (387) |
RP35 (953) |
RP55 (1986) |
RP75 (3470) |
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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: | COGs (COG3541) |
Previous IDs: | Nuc-transf; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
Number in seed: | 25 |
Number in full: | 1978 |
Average length of the domain: | 216.10 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 80.42 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 246 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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