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0  structures 4443  species 0  interactions 5026  sequences 15  architectures

Family: UPF0758_N (PF20582)

Summary: UPF0758 N-terminal

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.

UPF0758 N-terminal Provide feedback

This domain is functionally uncharacterised, found at the N-terminal of the uncharacterised UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG [1, 2]. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined [3]. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with PF04002 [4].

Literature references

  1. Lombardo MJ, Rosenberg SM; , J Bacteriol. 2000;182:6287-6291.: radC102 of Escherichia coli is an allele of recG. PUBMED:11053371 EPMC:11053371

  2. Attaiech L, Granadel C, Claverys JP, Martin B;, J Bacteriol. 2008;190:5729-5732.: RadC, a misleading name?. PUBMED:18556794 EPMC:18556794

  3. Ambroggio XI, Rees DC, Deshaies RJ;, PLoS Biol. 2004;2:E2.: JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. PUBMED:14737182 EPMC:14737182

  4. Iyer LM, Zhang D, Rogozin IB, Aravind L;, Nucleic Acids Res. 2011; [Epub ahead of print]: Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PUBMED:21890906 EPMC:21890906


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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
(742)
Full
(5026)
Representative proteomes UniProt
(25736)
RP15
(708)
RP35
(2540)
RP55
(5186)
RP75
(9023)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(742)
Full
(5026)
Representative proteomes UniProt
(25736)
RP15
(708)
RP35
(2540)
RP55
(5186)
RP75
(9023)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(742)
Full
(5026)
Representative proteomes UniProt
(25736)
RP15
(708)
RP35
(2540)
RP55
(5186)
RP75
(9023)
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

This family is new in this Pfam release.

Seed source: MGnify-UniProt clustering
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Paysan-Lafosse T , Chuguransky S
Number in seed: 742
Number in full: 5026
Average length of the domain: 77.8 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 33.63 %

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 27.1 27.1
Trusted cut-off 27.1 27.1
Noise cut-off 27.0 27.0
Model length: 78
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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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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
A0A0H3H4I9 View 3D Structure Click here
A0KEM8 View 3D Structure Click here
A0PZG4 View 3D Structure Click here
A1AV03 View 3D Structure Click here
A1B4F1 View 3D Structure Click here
A1BHA1 View 3D Structure Click here
A1K4J9 View 3D Structure Click here
A1S2D2 View 3D Structure Click here
A1SR15 View 3D Structure Click here
A1TTN2 View 3D Structure Click here
A1VSK8 View 3D Structure Click here
A1WBD9 View 3D Structure Click here
A1WIF4 View 3D Structure Click here
A1WZF2 View 3D Structure Click here
A2SJB0 View 3D Structure Click here
A3CN67 View 3D Structure Click here
A3N3Q8 View 3D Structure Click here
A3QIP9 View 3D Structure Click here
A4G7V9 View 3D Structure Click here
A4J7K6 View 3D Structure Click here
A4SFD1 View 3D Structure Click here
A4VGS8 View 3D Structure Click here
A4Y0K7 View 3D Structure Click here
A5G913 View 3D Structure Click here
A5I683 View 3D Structure Click here
A5N6I5 View 3D Structure Click here
A5URD0 View 3D Structure Click here
A6TFM9 View 3D Structure Click here
A6TQH8 View 3D Structure Click here
A6VK98 View 3D Structure Click here
A8ARM5 View 3D Structure Click here
A8AXK6 View 3D Structure Click here
A8FFU0 View 3D Structure Click here
A8H9B0 View 3D Structure Click here
A8MHM4 View 3D Structure Click here
A9BYK1 View 3D Structure Click here
A9IU27 View 3D Structure Click here
A9MKN7 View 3D Structure Click here
A9WAJ7 View 3D Structure Click here
B0CEV0 View 3D Structure Click here