Summary: alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 1
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alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 1 Provide feedback
An alpha helical domain related to the alpha-helical DNA glycosylases, predicted to catalyze the in situ synthesis of hypermodified bases such as alpha-glutamyl, putrescinyl thymine, 5-(2-aminoethoxy)methyluridine or 5-(2-aminoethyl)uridine. The enzyme is predicted to utilize a high-energy pyrophosphate DNA base intermediate which is subject to a nucleophilic attack by the modifying moiety. Members of this clade are found in phages with hypermodified bases and eukaryotes such as fungi and stramenopiles [1].
Literature references
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Iyer LM, Zhang D, Burroughs AM, Aravind L;, Nucleic Acids Res. 2013;41:7635-7655.: Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. PUBMED:23814188 EPMC:23814188
This tab holds annotation information from the InterPro database.
InterPro entry IPR040684
This entry represents an alpha helical domain related to the alpha-helical DNA glycosylases, predicted to catalyze the in situ synthesis of hypermodified bases such as alpha-glutamyl, putrescinyl thymine, 5-(2-aminoethoxy)methyluridine or 5-(2-aminoethyl)uridine. The enzyme is predicted to utilize a high-energy pyrophosphate DNA base intermediate which is subject to a nucleophilic attack by the modifying moiety. Members of this clade are found in phages with hypermodified bases and eukaryotes such as fungi and stramenopiles [ PUBMED:23814188 ].
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 aG_PT (CL0686), which has the following description:
This clan includes alpha-glutamyl/putrescinyl thymine phosphorylase related entries. According to sequence analysis several clades have been identified such as Clade-1, a prototypical aG/PT-pyrophoshorylase and Clade-2 pyrophoshorylases which are mainly found mainly in caudoviruses and prophages, where they are usually linked to a P-loop kinase. Several phages possess both a clade-1 aG/PT-pyrophoshorylase domain and a clade-2 protein [1].
The clan contains the following 3 members:
aGPT-Pplase1 aGPT-Pplase2 aGPT-Pplase3Alignments
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...
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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 (66) |
Full (349) |
Representative proteomes | UniProt (1043) |
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RP15 (126) |
RP35 (228) |
RP55 (340) |
RP75 (445) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (66) |
Full (349) |
Representative proteomes | UniProt (1043) |
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RP15 (126) |
RP35 (228) |
RP55 (340) |
RP75 (445) |
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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: | Iyer LM |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Iyer LM |
Number in seed: | 66 |
Number in full: | 349 |
Average length of the domain: | 261.3 aa |
Average identity of full alignment: | 29 % |
Average coverage of the sequence by the domain: | 63.58 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 281 | ||||||||||||
Family (HMM) version: | 4 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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