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50  structures 1342  species 0  interactions 9506  sequences 225  architectures

Family: ArgoL1 (PF08699)

Summary: Argonaute linker 1 domain

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.

Argonaute linker 1 domain Provide feedback

ArgoL1 is a region found in argonaute [1] proteins. It normally co-occurs with PF02179 and PF02171. It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel beta-sheet with two long beta-strands (beta8 and beta9) of the sheet spanning one face of the adjacent N and PAZ domains. L1 together with linker 2, L2, PAZ and ArgoN forms a compact global fold [2].

Literature references

  1. Hall TM; , Structure. 2005;13:1403-1408.: Structure and function of argonaute proteins. PUBMED:16216572 EPMC:16216572

  2. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T, Patel DJ;, Mol Cell. 2005;19:405-419.: Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. PUBMED:16061186 EPMC:16061186


This tab holds annotation information from the InterPro database.

InterPro entry IPR014811

ArgoL1 is a region found in argonaute [ PUBMED:16216572 ] proteins. It normally co-occurs with BAG domain ( INTERPRO ) and Piwi domain ( INTERPRO ). It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel beta-sheet with two long beta-strands (beta8 and beta9) of the sheet spanning one face of the adjacent N and PAZ domains. L1 together with linker 2, L2, PAZ and ArgoN forms a compact global fold [ PUBMED:16061186 ].

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
(225)
Full
(9506)
Representative proteomes UniProt
(13752)
RP15
(1307)
RP35
(3678)
RP55
(7088)
RP75
(9747)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(225)
Full
(9506)
Representative proteomes UniProt
(13752)
RP15
(1307)
RP35
(3678)
RP55
(7088)
RP75
(9747)
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
(225)
Full
(9506)
Representative proteomes UniProt
(13752)
RP15
(1307)
RP35
(3678)
RP55
(7088)
RP75
(9747)
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: Pfam-B_1585 (release 19.0)
Previous IDs: DUF1785;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Wood V
Number in seed: 225
Number in full: 9506
Average length of the domain: 50.80 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 5.71 %

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 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 51
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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 ArgoL1 domain has been found. There are 50 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
A0A0P0VLZ4 View 3D Structure Click here
A0A0P0W4J5 View 3D Structure Click here
A0A0R0I9G1 View 3D Structure Click here
A0A0R0JXM9 View 3D Structure Click here
A0A0R0KSC0 View 3D Structure Click here
A0A1D6DZF2 View 3D Structure Click here
A0A1D6E2V1 View 3D Structure Click here
A0A1D6EVH9 View 3D Structure Click here
A0A1D6F8V7 View 3D Structure Click here
A0A1D6FB88 View 3D Structure Click here
A0A1D6FWE3 View 3D Structure Click here
A0A1D6GFG2 View 3D Structure Click here
A0A1D6GKG3 View 3D Structure Click here
A0A1D6GWY2 View 3D Structure Click here
A0A1D6I0T3 View 3D Structure Click here
A0A1D6IAA8 View 3D Structure Click here
A0A1D6JCD6 View 3D Structure Click here
A0A1D6JEA5 View 3D Structure Click here
A0A1D6KWX6 View 3D Structure Click here
A0A1D6KZF1 View 3D Structure Click here
A0A1D6LIA5 View 3D Structure Click here
A0A1D6LSG3 View 3D Structure Click here
A0A1D6MEK7 View 3D Structure Click here
A0A1D6MQQ3 View 3D Structure Click here
A0A1D6P2M1 View 3D Structure Click here
A0A1D8PMK0 View 3D Structure Click here
A2CEI6 View 3D Structure Click here
A3KPK0 View 3D Structure Click here
D0EYF3 View 3D Structure Click here
D3ZRE1 View 3D Structure Click here
D3ZTP9 View 3D Structure Click here
D4AC38 View 3D Structure Click here
E7EXY4 View 3D Structure Click here
F1LUS2 View 3D Structure Click here
F1Q7S8 View 3D Structure Click here
G5ED77 View 3D Structure Click here
G5EES3 View 3D Structure Click here
I1JB56 View 3D Structure Click here
I1JIR2 View 3D Structure Click here
I1LDY9 View 3D Structure Click here