Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
87  structures 4670  species 0  interactions 6779  sequences 62  architectures

Family: GalKase_gal_bdg (PF10509)

Summary: Galactokinase galactose-binding signature

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.

Galactokinase galactose-binding signature Provide feedback

This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry [1]. The function of this domain appears to be to bind galactose [2] and the domain is normally at the N-terminus of the enzymes, EC:2.7.1.6 [3]. This domain is associated with the families GHMP_kinases_C, PF08544 and GHMP_kinases_N, PF00288.

Literature references

  1. Schalkwijk J, Wiedow O, Hirose S; , Biochem J. 1999;340:569-577.: The trappin gene family: proteins defined by an N-terminal transglutaminase substrate domain and a C-terminal four-disulphide core. PUBMED:10359639 EPMC:10359639

  2. Thoden JB, Holden HM; , J Biol Chem. 2003;278:33305-33311.: Molecular structure of galactokinase. PUBMED:12796487 EPMC:12796487

  3. Holden HM, Thoden JB, Timson DJ, Reece RJ; , Cell Mol Life Sci. 2004;61:2471-2484.: Galactokinase: structure, function and role in type II galactosemia. PUBMED:15526155 EPMC:15526155


This tab holds annotation information from the InterPro database.

InterPro entry IPR019539

This entry represents an N-terminal conserved domain found in all galactokinases, irrespective of how many other ATP binding sites, etc that they carry [ PUBMED:10359639 ]. The function of this domain appears to be to bind galactose [ PUBMED:12796487 ], and it is normally located at the N terminus of these enzymes [ PUBMED:15526155 ]. It is associated with INTERPRO and INTERPRO . While all enzymes in this entry posses galactokinase activity, some are annotated as N-acetylgalactosamine kinases as they also posses this enzyme activity.

This domain can also be found in mevalonate kinase and related proteins from all domains of life. It can also be found in arabinose kinase from Arabidopsis [ PUBMED:10344205 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N

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
(465)
Full
(6779)
Representative proteomes UniProt
(24488)
RP15
(948)
RP35
(3186)
RP55
(6323)
RP75
(10163)
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
(465)
Full
(6779)
Representative proteomes UniProt
(24488)
RP15
(948)
RP35
(3186)
RP55
(6323)
RP75
(10163)
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
(465)
Full
(6779)
Representative proteomes UniProt
(24488)
RP15
(948)
RP35
(3186)
RP55
(6323)
RP75
(10163)
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: PROSITE_PS00106, Pfam-B_2277 (release 22.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Coggill P
Number in seed: 465
Number in full: 6779
Average length of the domain: 48.90 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 11.18 %

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 23.1 23.1
Trusted cut-off 23.1 23.1
Noise cut-off 23.0 23.0
Model length: 50
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

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 GalKase_gal_bdg domain has been found. There are 87 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.

Loading structure mapping...

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
A0A0R0J3A5 View 3D Structure Click here
A0A1D6E029 View 3D Structure Click here
A0A1D6GVC9 View 3D Structure Click here
A0A1D6LAE7 View 3D Structure Click here
A0A1D6QT52 View 3D Structure Click here
A0A368UI64 View 3D Structure Click here
A4IBE2 View 3D Structure Click here
E7FDP4 View 3D Structure Click here
F1R3T4 View 3D Structure Click here
I1KMP3 View 3D Structure Click here
I1KPR8 View 3D Structure Click here
I1M9V9 View 3D Structure Click here
I1MRT3 View 3D Structure Click here
I1MWC4 View 3D Structure Click here
O01969 View 3D Structure Click here
O23461 View 3D Structure Click here
P04385 View 3D Structure Click here
P0A6T3 View 3D Structure Click here
P13045 View 3D Structure Click here
P51570 View 3D Structure Click here
P9WN63 View 3D Structure Click here
Q01415 View 3D Structure Click here
Q0JAB2 View 3D Structure Click here
Q4DC09 View 3D Structure Click here
Q4DF18 View 3D Structure Click here
Q4DFH6 View 3D Structure Click here
Q4DHU8 View 3D Structure Click here
Q54DN6 View 3D Structure Click here
Q59VY8 View 3D Structure Click here
Q5RKH2 View 3D Structure Click here
Q5XIG6 View 3D Structure Click here
Q68FH4 View 3D Structure Click here
Q6YX79 View 3D Structure Click here
Q7Y152 View 3D Structure Click here
Q8VYG2 View 3D Structure Click here
Q95U34 View 3D Structure Click here
Q9HDU2 View 3D Structure Click here
Q9R0N0 View 3D Structure Click here
Q9SEE5 View 3D Structure Click here