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454  structures 8461  species 0  interactions 52528  sequences 327  architectures

Family: PfkB (PF00294)

Summary: pfkB family carbohydrate kinase

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.

pfkB family carbohydrate kinase Provide feedback

This family includes a variety of carbohydrate and pyrimidine kinases.

Literature references

  1. Petersen LA, Downs DM; , J Bacteriol 1997;179:4894-4900.: Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis. PUBMED:9519409 EPMC:9519409


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011611

This domain is found in a variety of carbohydrate and pyrimidine kinases. It is found in phosphomethylpyrimidine kinase ( EC ), which is part of the thiamine pyrophosphate (TPP) synthesis pathway - TPP being an essential cofactor for many enzymes [ PUBMED:9519409 ]. It is also found in 2-keto-3-deoxygluconate kinase, which is a component of the Entner-Doudoroff pathway in hyperthermophilic archaea [ PUBMED:15869466 ].

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 Ribokinase (CL0118), which has the following description:

All of these enzymes are phosphotransferases that have an alcohol group as an acceptor (EC:2.7.1.-). However, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase) catalyses two phosphorylation reactions: one to a hydroxymethyl group of hydroxymethyl pyrimidine (HMP) and the second to the phosphomethyl group of HMPP [1]. The common structural feature for the enzymes in this superfamily is a central eight-stranded sheet that is flanked by eight structurally conserved helices, five on one side and three on the other [1]. The active site is located in a shallow groove along one edge of the sheet, with the phosphate acceptor hydroxyl group and -phosphate of ATP close together in the middle of the groove, and substrate and ATP binding at the ends [1].

The clan contains the following 5 members:

ADP_PFK_GK Carb_kinase HK PfkB Phos_pyr_kin

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
(50)
Full
(52528)
Representative proteomes UniProt
(234312)
RP15
(6330)
RP35
(24099)
RP55
(51077)
RP75
(87883)
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
(50)
Full
(52528)
Representative proteomes UniProt
(234312)
RP15
(6330)
RP35
(24099)
RP55
(51077)
RP75
(87883)
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
(50)
Full
(52528)
Representative proteomes UniProt
(234312)
RP15
(6330)
RP35
(24099)
RP55
(51077)
RP75
(87883)
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: Prosite
Previous IDs: pfkB;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD , Griffiths-Jones SR
Number in seed: 50
Number in full: 52528
Average length of the domain: 272.20 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 82.73 %

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 25.8 25.8
Trusted cut-off 25.8 25.8
Noise cut-off 25.7 25.7
Model length: 302
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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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 PfkB domain has been found. There are 454 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
A0A0N7KRX2 View 3D Structure Click here
A0A0R0E4L0 View 3D Structure Click here
A0A0R0EBJ8 View 3D Structure Click here
A0A0R0ENJ3 View 3D Structure Click here
A0A0R0FEB3 View 3D Structure Click here
A0A0R0G0T0 View 3D Structure Click here
A0A0R0GU87 View 3D Structure Click here
A0A0R0HP60 View 3D Structure Click here
A0A0R0HP60 View 3D Structure Click here
A0A0R0I8N3 View 3D Structure Click here
A0A0R0IF88 View 3D Structure Click here
A0A0R0KL40 View 3D Structure Click here
A0A0R4IIH9 View 3D Structure Click here
A0A1D6E5Z5 View 3D Structure Click here
A0A1D6FCK2 View 3D Structure Click here
A0A1D6FMZ6 View 3D Structure Click here
A0A1D6FMZ6 View 3D Structure Click here
A0A1D6G0Z9 View 3D Structure Click here
A0A1D6JPP2 View 3D Structure Click here
A0A1D6JPP2 View 3D Structure Click here
A0A1D6KIN1 View 3D Structure Click here
A0A1D6KIN1 View 3D Structure Click here
A0A1D6KWT3 View 3D Structure Click here
A0A1D6N511 View 3D Structure Click here
A0A1D6N726 View 3D Structure Click here
A0A1D8PCJ7 View 3D Structure Click here
A0A1D8PFI3 View 3D Structure Click here
A0A1D8PFI3 View 3D Structure Click here
A0A1D8PKZ6 View 3D Structure Click here
A0A1D8PQ26 View 3D Structure Click here
A0A368UHI5 View 3D Structure Click here
A0A368UHI5 View 3D Structure Click here
A1A6H3 View 3D Structure Click here
A4I2M8 View 3D Structure Click here
A4I5C0 View 3D Structure Click here
A4IAC6 View 3D Structure Click here
B4FEH1 View 3D Structure Click here
B4FFH8 View 3D Structure Click here
B4FRB2 View 3D Structure Click here
B4FVM5 View 3D Structure Click here
B6U666 View 3D Structure Click here
B9FSC3 View 3D Structure Click here
C6T7F3 View 3D Structure Click here
C6TGN8 View 3D Structure Click here
C6TNU7 View 3D Structure Click here
D3ZVU4 View 3D Structure Click here
E9AHA4 View 3D Structure Click here
F1QCR8 View 3D Structure Click here
F1QM18 View 3D Structure Click here
F1RCK7 View 3D Structure Click here
F4I0K2 View 3D Structure Click here
F4JM15 View 3D Structure Click here
F4JM15 View 3D Structure Click here
F4K7C7 View 3D Structure Click here
F4K7C7 View 3D Structure Click here
I1J631 View 3D Structure Click here
I1J756 View 3D Structure Click here
I1JEH3 View 3D Structure Click here
I1JPN3 View 3D Structure Click here
I1L6S1 View 3D Structure Click here
I1L8B4 View 3D Structure Click here
I1LC17 View 3D Structure Click here
I1LDW8 View 3D Structure Click here
I1LJP3 View 3D Structure Click here
I1LP63 View 3D Structure Click here
I1LYG8 View 3D Structure Click here
I1LYQ6 View 3D Structure Click here
I1LYQ6 View 3D Structure Click here
I1LZ92 View 3D Structure Click here
I1M2U6 View 3D Structure Click here
I1M561 View 3D Structure Click here
I1M8A6 View 3D Structure Click here
I1MBA8 View 3D Structure Click here
I1MD61 View 3D Structure Click here
I1MIW3 View 3D Structure Click here
I1MXX4 View 3D Structure Click here
I1NA97 View 3D Structure Click here
I1NDC7 View 3D Structure Click here
I1NDC7 View 3D Structure Click here
I1NID2 View 3D Structure Click here
K7KA65 View 3D Structure Click here
K7KFL0 View 3D Structure Click here
K7KFL0 View 3D Structure Click here
K7KFL3 View 3D Structure Click here
K7KFL3 View 3D Structure Click here
K7LP39 View 3D Structure Click here
K7LT57 View 3D Structure Click here
K7LZE4 View 3D Structure Click here
K7LZE4 View 3D Structure Click here
K7M8F8 View 3D Structure Click here
K7UH13 View 3D Structure Click here
K7VC50 View 3D Structure Click here
K7VK13 View 3D Structure Click here
O01824 View 3D Structure Click here
O60116 View 3D Structure Click here
O77425 View 3D Structure Click here
O82616 View 3D Structure Click here
P06999 View 3D Structure Click here
P0A0B9 View 3D Structure Click here
P0A9J6 View 3D Structure Click here
P0AEW6 View 3D Structure Click here
P0AEW9 View 3D Structure Click here
P23060 View 3D Structure Click here
P25332 View 3D Structure Click here
P30235 View 3D Structure Click here
P32143 View 3D Structure Click here
P33020 View 3D Structure Click here
P37647 View 3D Structure Click here
P45543 View 3D Structure Click here
P47143 View 3D Structure Click here
P50053 View 3D Structure Click here
P55263 View 3D Structure Click here
P55264 View 3D Structure Click here
P71913 View 3D Structure Click here
P76419 View 3D Structure Click here
P76658 View 3D Structure Click here
P77493 View 3D Structure Click here
P78825 View 3D Structure Click here
P97328 View 3D Structure Click here
P9WID3 View 3D Structure Click here
P9WID5 View 3D Structure Click here
Q02974 View 3D Structure Click here
Q09839 View 3D Structure Click here
Q0DZE5 View 3D Structure Click here
Q0J8G4 View 3D Structure Click here
Q0JBQ0 View 3D Structure Click here
Q0JGZ6 View 3D Structure Click here
Q19133 View 3D Structure Click here
Q22721 View 3D Structure Click here
Q2FWM2 View 3D Structure Click here
Q2G164 View 3D Structure Click here
Q2G1A6 View 3D Structure Click here
Q2G238 View 3D Structure Click here
Q4CVK9 View 3D Structure Click here
Q4CY14 View 3D Structure Click here
Q4CYT2 View 3D Structure Click here
Q4E0S4 View 3D Structure Click here
Q4E4K4 View 3D Structure Click here
Q54D80 View 3D Structure Click here
Q54MB5 View 3D Structure Click here
Q54Q47 View 3D Structure Click here
Q54UQ4 View 3D Structure Click here
Q55FH2 View 3D Structure Click here
Q57849 View 3D Structure Click here
Q58732 View 3D Structure Click here
Q5GA22 View 3D Structure Click here
Q5N7A1 View 3D Structure Click here
Q5SN59 View 3D Structure Click here
Q60F00 View 3D Structure Click here
Q60F00 View 3D Structure Click here
Q64640 View 3D Structure Click here
Q657Z1 View 3D Structure Click here
Q6AVL0 View 3D Structure Click here
Q6P3J9 View 3D Structure Click here
Q6XZ78 View 3D Structure Click here
Q6XZ79 View 3D Structure Click here
Q6Z1P3 View 3D Structure Click here
Q6Z1P3 View 3D Structure Click here
Q7JWW6 View 3D Structure Click here
Q7XBZ0 View 3D Structure Click here
Q84R36 View 3D Structure Click here
Q8R1Q9 View 3D Structure Click here
Q8S5U3 View 3D Structure Click here
Q8T3U8 View 3D Structure Click here
Q8T4I0 View 3D Structure Click here
Q93934 View 3D Structure Click here
Q93Z01 View 3D Structure Click here
Q940Y6 View 3D Structure Click here
Q94AT3 View 3D Structure Click here
Q94AT3 View 3D Structure Click here
Q9C524 View 3D Structure Click here
Q9FLH8 View 3D Structure Click here
Q9H477 View 3D Structure Click here
Q9LN35 View 3D Structure Click here
Q9LNE3 View 3D Structure Click here
Q9LNE4 View 3D Structure Click here
Q9LZG0 View 3D Structure Click here
Q9M1B9 View 3D Structure Click here
Q9M394 View 3D Structure Click here
Q9SF85 View 3D Structure Click here
Q9SID0 View 3D Structure Click here
Q9SX54 View 3D Structure Click here
Q9USY1 View 3D Structure Click here
Q9USY1 View 3D Structure Click here
Q9VK96 View 3D Structure Click here
Q9VPR3 View 3D Structure Click here
Q9VTI3 View 3D Structure Click here
Q9VU38 View 3D Structure Click here
Q9VW82 View 3D Structure Click here
Q9VW84 View 3D Structure Click here