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409  structures 8086  species 0  interactions 52776  sequences 4048  architectures

Family: ketoacyl-synt (PF00109)

Summary: Beta-ketoacyl synthase, N-terminal domain

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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.

Beta-ketoacyl synthase, N-terminal domain Provide feedback

The structure of beta-ketoacyl synthase is similar to that of the thiolase family (PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine [1].

Literature references

  1. Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y; , EMBO J 1998;17:1183-1191.: Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes. PUBMED:9482715 EPMC:9482715


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014030

Beta-ketoacyl-ACP synthase EC (KAS) [ PUBMED:3076376 ] is the enzyme that catalyzes the condensation of malonyl-ACP with the growing fatty acid chain. It is found as a component of a number of enzymatic systems, including fatty acid synthetase (FAS), which catalyzes the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH; the multi-functional 6-methysalicylic acid synthase (MSAS) from Penicillium patulum [ PUBMED:2209605 ], which is involved in the biosynthesis of a polyketide antibiotic; polyketide antibiotic synthase enzyme systems; Emericella nidulans multifunctional protein Wa, which is involved in the biosynthesis of conidial green pigment; Rhizobium nodulation protein nodE, which probably acts as a beta-ketoacyl synthase in the synthesis of the nodulation Nod factor fatty acyl chain; and yeast mitochondrial protein CEM1. The condensation reaction is a two step process, first the acyl component of an activated acyl primer is transferred to a cysteine residue of the enzyme and is then condensed with an activated malonyl donor with the concomitant release of carbon dioxide.

This entry represents the N-terminal domain of beta-ketoacyl-ACP synthases.

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 Thiolase (CL0046), which has the following description:

Thiolases are ubiquitous and form a large superfamily. Thiolases can function either degradatively, in the beta-oxidation pathway of fatty acids, or biosynthetically. Biosynthetic thiolases catalyse the formation of acetoacetyl-CoA from two molecules of acetyl-CoA . This is one of the fundamental categories of carbon skeletal assembly patterns in biological systems and is the first step in a wide range of biosynthetic pathways [1]. Thiolase are usually dimeric or tetrameric enzymes. Within each monomer there are two similar domains related by pseudo dyad. The N-terminal of these two domains contains a large insertion of about 100 amino acids.

The clan contains the following 14 members:

ACP_syn_III ACP_syn_III_C Chal_sti_synt_C Chal_sti_synt_N FAE1_CUT1_RppA HMG_CoA_synt_C HMG_CoA_synt_N KAsynt_C_assoc ketoacyl-synt Ketoacyl-synt_2 Ketoacyl-synt_C SpoVAD Thiolase_C Thiolase_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
(77)
Full
(52776)
Representative proteomes UniProt
(211647)
RP15
(5814)
RP35
(21840)
RP55
(49146)
RP75
(86029)
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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
(77)
Full
(52776)
Representative proteomes UniProt
(211647)
RP15
(5814)
RP35
(21840)
RP55
(49146)
RP75
(86029)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(77)
Full
(52776)
Representative proteomes UniProt
(211647)
RP15
(5814)
RP35
(21840)
RP55
(49146)
RP75
(86029)
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: Dotter
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Griffiths-Jones SR
Number in seed: 77
Number in full: 52776
Average length of the domain: 234.20 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 19.11 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 253
Family (HMM) version: 28
Download: download the raw HMM for this family

Species distribution

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Selections

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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 ketoacyl-synt domain has been found. There are 409 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
A0A089QRB9 View 3D Structure Click here
A0A0R0GE20 View 3D Structure Click here
A0A1D6F1P1 View 3D Structure Click here
A0A1D6H430 View 3D Structure Click here
A0A1D6IJN4 View 3D Structure Click here
A0A1D6LUH4 View 3D Structure Click here
A0A1D8PK65 View 3D Structure Click here
A4I9B2 View 3D Structure Click here
B0G100 View 3D Structure Click here
B0G101 View 3D Structure Click here
B0G103 View 3D Structure Click here
B0G170 View 3D Structure Click here
B7F6I0 View 3D Structure Click here
B7Z001 View 3D Structure Click here
C0PGF8 View 3D Structure Click here
C6KT99 View 3D Structure Click here
E7F5V3 View 3D Structure Click here
F1R7W6 View 3D Structure Click here
G3V6R7 View 3D Structure Click here
I1K678 View 3D Structure Click here
I1KPM3 View 3D Structure Click here
I1L8I1 View 3D Structure Click here
I1LYQ3 View 3D Structure Click here
I1N0K0 View 3D Structure Click here
I6X8D2 View 3D Structure Click here
I6Y231 View 3D Structure Click here
K7MWV4 View 3D Structure Click here
K7V9P7 View 3D Structure Click here
M9PB21 View 3D Structure Click here
O06586 View 3D Structure Click here
O06586 View 3D Structure Click here
O53901 View 3D Structure Click here
O65933 View 3D Structure Click here
O86335 View 3D Structure Click here
O94297 View 3D Structure Click here
P0A953 View 3D Structure Click here
P0AAI5 View 3D Structure Click here
P0C842 View 3D Structure Click here
P12785 View 3D Structure Click here
P19096 View 3D Structure Click here
P19097 View 3D Structure Click here
P39525 View 3D Structure Click here
P49327 View 3D Structure Click here
P52410 View 3D Structure Click here
P71718 View 3D Structure Click here
P91866 View 3D Structure Click here
P91871 View 3D Structure Click here
P94996 View 3D Structure Click here
P96202 View 3D Structure Click here
P96284 View 3D Structure Click here
P9WQD7 View 3D Structure Click here
P9WQD9 View 3D Structure Click here
P9WQE1 View 3D Structure Click here
P9WQE3 View 3D Structure Click here
P9WQE5 View 3D Structure Click here
P9WQE7 View 3D Structure Click here
P9WQE9 View 3D Structure Click here
Q0E328 View 3D Structure Click here
Q10289 View 3D Structure Click here
Q2FZR9 View 3D Structure Click here
Q4DFM5 View 3D Structure Click here
Q4DGN7 View 3D Structure Click here
Q54D44 View 3D Structure Click here
Q54ED6 View 3D Structure Click here
Q54ED7 View 3D Structure Click here
Q54FQ1 View 3D Structure Click here
Q54G30 View 3D Structure Click here
Q54IX3 View 3D Structure Click here
Q54KA0 View 3D Structure Click here
Q54KU3 View 3D Structure Click here
Q54KU5 View 3D Structure Click here
Q54QD1 View 3D Structure Click here
Q54QD3 View 3D Structure Click here
Q554C4 View 3D Structure Click here
Q559A9 View 3D Structure Click here
Q5ANC6 View 3D Structure Click here
Q5ECI4 View 3D Structure Click here
Q5ECI5 View 3D Structure Click here
Q69YA2 View 3D Structure Click here
Q6A1T5 View 3D Structure Click here
Q7PLB8 View 3D Structure Click here
Q869W9 View 3D Structure Click here
Q869X2 View 3D Structure Click here
Q86JI5 View 3D Structure Click here
Q8H3I6 View 3D Structure Click here
Q8L3X9 View 3D Structure Click here
Q9C9P4 View 3D Structure Click here
Q9D404 View 3D Structure Click here
Q9M507 View 3D Structure Click here
Q9M508 View 3D Structure Click here
Q9NWU1 View 3D Structure Click here
Q9VNF5 View 3D Structure Click here
U3JAJ7 View 3D Structure Click here