Summary: Galactokinase galactose-binding signature
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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
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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
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Thoden JB, Holden HM; , J Biol Chem. 2003;278:33305-33311.: Molecular structure of galactokinase. PUBMED:12796487 EPMC:12796487
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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...
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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_NAlignments
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...
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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 (463) |
Full (7191) |
Representative proteomes | UniProt (26207) |
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RP15 (1047) |
RP35 (3404) |
RP55 (6775) |
RP75 (10898) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
— not available.
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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 (463) |
Full (7191) |
Representative proteomes | UniProt (26207) |
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RP15 (1047) |
RP35 (3404) |
RP55 (6775) |
RP75 (10898) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | PROSITE_PS00106, Pfam-B_2277 (release 22.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 463 |
Number in full: | 7191 |
Average length of the domain: | 48.9 aa |
Average identity of full alignment: | 40 % |
Average coverage of the sequence by the domain: | 11.14 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 50 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 GalKase_gal_bdg domain has been found. There are 95 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.