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64  structures 8157  species 0  interactions 55426  sequences 412  architectures

Family: Glyco_transf_4 (PF13439)

Summary: Glycosyltransferase Family 4

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.

Glycosyltransferase Family 4 Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR028098

MshA belongs to the GT-B structural family of glycosyltransferases whose members have a two-domain structure with both domains exhibiting a Rossman-type fold [ PUBMED:18390549 ]. This entry represents the N-terminal domain found in MshA and the subfamily 4 of glycosyltransferases family 1.

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
(913)
Full
(55426)
Representative proteomes UniProt
(261910)
RP15
(7283)
RP35
(26601)
RP55
(56274)
RP75
(95622)
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
(913)
Full
(55426)
Representative proteomes UniProt
(261910)
RP15
(7283)
RP35
(26601)
RP55
(56274)
RP75
(95622)
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
(913)
Full
(55426)
Representative proteomes UniProt
(261910)
RP15
(7283)
RP35
(26601)
RP55
(56274)
RP75
(95622)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Jackhmmer:Q2Y6X7
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 913
Number in full: 55426
Average length of the domain: 165.70 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 40.45 %

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 28.5 28.5
Trusted cut-off 28.5 28.5
Noise cut-off 28.4 28.4
Model length: 170
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Glyco_transf_4 domain has been found. There are 64 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
A0A0R0GUJ0 View 3D Structure Click here
A0A0R0J9M2 View 3D Structure Click here
A0A1D6E1K2 View 3D Structure Click here
A0A1D6FE39 View 3D Structure Click here
A0A1D6JX85 View 3D Structure Click here
A0A1D6NHE4 View 3D Structure Click here
A0A1D6PE22 View 3D Structure Click here
A0A1D6PIW6 View 3D Structure Click here
C6TI07 View 3D Structure Click here
F1QPS1 View 3D Structure Click here
F4IBV4 View 3D Structure Click here
F4JT73 View 3D Structure Click here
G3V6U3 View 3D Structure Click here
G5ECB6 View 3D Structure Click here
I1J786 View 3D Structure Click here
I1J850 View 3D Structure Click here
I1JLR0 View 3D Structure Click here
I1L595 View 3D Structure Click here
I1MLY2 View 3D Structure Click here
I1MMI1 View 3D Structure Click here
I1N2U7 View 3D Structure Click here
K7M3G4 View 3D Structure Click here
P25740 View 3D Structure Click here
P27127 View 3D Structure Click here
P43636 View 3D Structure Click here
P71237 View 3D Structure Click here
P71243 View 3D Structure Click here
P96407 View 3D Structure Click here
P9WMY5 View 3D Structure Click here
P9WMY7 View 3D Structure Click here
P9WMY9 View 3D Structure Click here
P9WMZ1 View 3D Structure Click here
P9WMZ3 View 3D Structure Click here
P9WMZ5 View 3D Structure Click here
Q10QW6 View 3D Structure Click here
Q19265 View 3D Structure Click here
Q2G1K0 View 3D Structure Click here
Q2G255 View 3D Structure Click here
Q2G290 View 3D Structure Click here
Q4D163 View 3D Structure Click here
Q4DXT6 View 3D Structure Click here
Q4E588 View 3D Structure Click here
Q54GL6 View 3D Structure Click here
Q58469 View 3D Structure Click here
Q58577 View 3D Structure Click here
Q59LF2 View 3D Structure Click here
Q5VPB6 View 3D Structure Click here
Q5ZBM2 View 3D Structure Click here
Q69LA5 View 3D Structure Click here
Q7KWM5 View 3D Structure Click here
Q7XLZ9 View 3D Structure Click here
Q84QB1 View 3D Structure Click here
Q8S4F6 View 3D Structure Click here
Q96WW6 View 3D Structure Click here
Q9CAT1 View 3D Structure Click here
Q9DBE8 View 3D Structure Click here
Q9H553 View 3D Structure Click here
Q9VEE9 View 3D Structure Click here
Q9VZU8 View 3D Structure Click here