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314  structures 8815  species 0  interactions 39523  sequences 327  architectures

Family: HGTP_anticodon (PF03129)

Summary: Anticodon binding 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.

Anticodon binding domain Provide feedback

This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [1] it is probably the anticodon binding domain [2].

Literature references

  1. Wolf YI, Aravind L, Grishin NV, Koonin EV; , Genome Res 1999;9:689-710.: Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. PUBMED:10447505 EPMC:10447505

  2. Aberg A, Yaremchuk A, Tukalo M, Rasmussen B, Cusack S; , Biochemistry 1997;36:3084-3094.: Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase. PUBMED:9115984 EPMC:9115984


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004154

tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [ PUBMED:10447505 ]. It is probably the anticodon binding domain [ PUBMED:9115984 ].

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 IIaaRS-ABD (CL0458), which has the following description:

This superfamily is characterised by including the anticodon-binding domain of Class II aaRS and the Brix domain.

The clan contains the following 3 members:

Brix HGTP_anticodon HGTP_anticodon2

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
(97)
Full
(39523)
Representative proteomes UniProt
(166618)
RP15
(6142)
RP35
(19174)
RP55
(37902)
RP75
(61215)
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
(97)
Full
(39523)
Representative proteomes UniProt
(166618)
RP15
(6142)
RP35
(19174)
RP55
(37902)
RP75
(61215)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(97)
Full
(39523)
Representative proteomes UniProt
(166618)
RP15
(6142)
RP35
(19174)
RP55
(37902)
RP75
(61215)
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: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 97
Number in full: 39523
Average length of the domain: 92.90 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 16.42 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 94
Family (HMM) version: 22
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 HGTP_anticodon domain has been found. There are 314 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
A0A0G2JZI2 View 3D Structure Click here
A0A0R0FFI0 View 3D Structure Click here
A0A0R4ISX2 View 3D Structure Click here
A0A144A0G8 View 3D Structure Click here
A0A1D6E223 View 3D Structure Click here
A0A1D6EC22 View 3D Structure Click here
A0A1D6FUK0 View 3D Structure Click here
A0A1D6GJU2 View 3D Structure Click here
A0A1D6GKX7 View 3D Structure Click here
A0A1D6HMF9 View 3D Structure Click here
A0A1D6HSW9 View 3D Structure Click here
A0A1D6II54 View 3D Structure Click here
A0A1D6KKI8 View 3D Structure Click here
A0A1D6KSQ7 View 3D Structure Click here
A0A1D6LIU0 View 3D Structure Click here
A0A1D6MIP9 View 3D Structure Click here
A0A1D8PCV0 View 3D Structure Click here
A0A1D8PMV9 View 3D Structure Click here
A0A1D8PRZ3 View 3D Structure Click here
A2BIM7 View 3D Structure Click here
A2RTX5 View 3D Structure Click here
A4HXZ5 View 3D Structure Click here
A4HY00 View 3D Structure Click here
A4I591 View 3D Structure Click here
A4IB34 View 3D Structure Click here
A4ID12 View 3D Structure Click here
C0PGQ1 View 3D Structure Click here
D3ZYP7 View 3D Structure Click here
E7F4P9 View 3D Structure Click here
E9QI36 View 3D Structure Click here
F1M9C9 View 3D Structure Click here
F1Q6U0 View 3D Structure Click here
F1QHZ4 View 3D Structure Click here
F1QP23 View 3D Structure Click here
F1QUV7 View 3D Structure Click here
F4IAM7 View 3D Structure Click here
F4IFC5 View 3D Structure Click here
F4IYF8 View 3D Structure Click here
I1J5B4 View 3D Structure Click here
I1JC08 View 3D Structure Click here
I1JPP8 View 3D Structure Click here
I1JQX3 View 3D Structure Click here
I1KQ70 View 3D Structure Click here
I1KZJ9 View 3D Structure Click here
I1L332 View 3D Structure Click here
I1MPJ4 View 3D Structure Click here
I1NAJ0 View 3D Structure Click here
I1NBI4 View 3D Structure Click here
K7KRK6 View 3D Structure Click here
K7LK13 View 3D Structure Click here
K7UDG5 View 3D Structure Click here
O04630 View 3D Structure Click here
O13969 View 3D Structure Click here
O23627 View 3D Structure Click here
O43011 View 3D Structure Click here
O45869 View 3D Structure Click here
O60155 View 3D Structure Click here
O74765 View 3D Structure Click here
O82413 View 3D Structure Click here
P04801 View 3D Structure Click here
P07236 View 3D Structure Click here
P07263 View 3D Structure Click here
P07814 View 3D Structure Click here
P0A8M3 View 3D Structure Click here
P12081 View 3D Structure Click here
P16659 View 3D Structure Click here
P26639 View 3D Structure Click here
P28668 View 3D Structure Click here
P34183 View 3D Structure Click here
P38088 View 3D Structure Click here
P38708 View 3D Structure Click here
P41250 View 3D Structure Click here
P49590 View 3D Structure Click here
P52709 View 3D Structure Click here
P60906 View 3D Structure Click here
P87144 View 3D Structure Click here
P93422 View 3D Structure Click here
P9WFT5 View 3D Structure Click here
P9WFT9 View 3D Structure Click here
P9WFV5 View 3D Structure Click here
P9WFV7 View 3D Structure Click here
Q06817 View 3D Structure Click here
Q0D8E4 View 3D Structure Click here
Q0JDK3 View 3D Structure Click here
Q10039 View 3D Structure Click here
Q10179 View 3D Structure Click here
Q22620 View 3D Structure Click here
Q2FXP7 View 3D Structure Click here
Q2FXU4 View 3D Structure Click here
Q2FY08 View 3D Structure Click here
Q2G1Z4 View 3D Structure Click here
Q2QS11 View 3D Structure Click here
Q3UQ84 View 3D Structure Click here
Q4D449 View 3D Structure Click here
Q4D9G6 View 3D Structure Click here
Q4DA54 View 3D Structure Click here
Q4DLK5 View 3D Structure Click here
Q4DNQ1 View 3D Structure Click here
Q4DPR0 View 3D Structure Click here
Q4DZZ4 View 3D Structure Click here
Q4QQV4 View 3D Structure Click here
Q54J66 View 3D Structure Click here
Q54PF9 View 3D Structure Click here
Q54Q07 View 3D Structure Click here
Q55D12 View 3D Structure Click here
Q57681 View 3D Structure Click here
Q58406 View 3D Structure Click here
Q58597 View 3D Structure Click here
Q58635 View 3D Structure Click here
Q59R20 View 3D Structure Click here
Q5A2A5 View 3D Structure Click here
Q5AJX0 View 3D Structure Click here
Q5I0G4 View 3D Structure Click here
Q5M7W7 View 3D Structure Click here
Q5XHY5 View 3D Structure Click here
Q61035 View 3D Structure Click here
Q68FW7 View 3D Structure Click here
Q6ER90 View 3D Structure Click here
Q6Z0N5 View 3D Structure Click here
Q6Z695 View 3D Structure Click here
Q6ZD35 View 3D Structure Click here
Q7L3T8 View 3D Structure Click here
Q86AS6 View 3D Structure Click here
Q8BLY2 View 3D Structure Click here
Q8CFI5 View 3D Structure Click here
Q8CGC7 View 3D Structure Click here
Q8GZ45 View 3D Structure Click here
Q8IIA4 View 3D Structure Click here
Q8IL22 View 3D Structure Click here
Q8ILP6 View 3D Structure Click here
Q8IQX8 View 3D Structure Click here
Q8MP20 View 3D Structure Click here
Q99KK9 View 3D Structure Click here
Q9BW92 View 3D Structure Click here
Q9CZD3 View 3D Structure Click here
Q9D0R2 View 3D Structure Click here
Q9FYR6 View 3D Structure Click here
Q9LEV2 View 3D Structure Click here
Q9M1R2 View 3D Structure Click here
Q9QZM2 View 3D Structure Click here
Q9U9Q2 View 3D Structure Click here
Q9UHN1 View 3D Structure Click here
Q9VJV8 View 3D Structure Click here
Q9VKB0 View 3D Structure Click here
Q9VUK8 View 3D Structure Click here
Q9VZY9 View 3D Structure Click here