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0  structures 317  species 0  interactions 4581  sequences 60  architectures

Family: FAE1_CUT1_RppA (PF08392)

Summary: FAE1/Type III polyketide synthase-like protein

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.

FAE1/Type III polyketide synthase-like protein Provide feedback

The members of this family are described as 3-ketoacyl-CoA synthases, type III polyketide synthases, fatty acid elongases and fatty acid condensing enzymes, and are found in both prokaryotic and eukaryotic (mainly plant) species. The region featured in this family contains the active site residues, as well as motifs involved in substrate binding [1].

Literature references

  1. Funa N, Ohnishi Y, Ebizuka Y, Horinouchi S; , Biochem J 2002;367:781-789.: Alteration of reaction and substrate specificity of a bacterial type III polyketide synthase by site-directed mutagenesis. PUBMED:12139488 EPMC:12139488


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013601

This domain is found in proteins that are described as 3-ketoacyl-CoA synthases, type III polyketide synthases, fatty acid elongases and fatty acid condensing enzymes, and are found in both prokaryotic and eukaryotic (mainly plant) species. The region contains the active site residues, as well as motifs involved in substrate binding [ PUBMED:12139488 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(22)
Full
(4581)
Representative proteomes UniProt
(7663)
RP15
(485)
RP35
(2546)
RP55
(3910)
RP75
(5096)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(22)
Full
(4581)
Representative proteomes UniProt
(7663)
RP15
(485)
RP35
(2546)
RP55
(3910)
RP75
(5096)
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
(22)
Full
(4581)
Representative proteomes UniProt
(7663)
RP15
(485)
RP35
(2546)
RP55
(3910)
RP75
(5096)
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: Pfam-B_1177 (release 18.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Fenech M
Number in seed: 22
Number in full: 4581
Average length of the domain: 249.00 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 57.79 %

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 20.1 20.1
Trusted cut-off 20.1 20.1
Noise cut-off 20.0 20.0
Model length: 290
Family (HMM) version: 14
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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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
A0A0N7KG16 View 3D Structure Click here
A0A0P0VTE3 View 3D Structure Click here
A0A0P0WUT4 View 3D Structure Click here
A0A0P0X4C2 View 3D Structure Click here
A0A0P0XQP0 View 3D Structure Click here
A0A0R0EFL7 View 3D Structure Click here
A0A0R0I9A1 View 3D Structure Click here
A0A0R0IP41 View 3D Structure Click here
A0A1D6EMK3 View 3D Structure Click here
A0A1D6GQJ7 View 3D Structure Click here
A0A1D6HP46 View 3D Structure Click here
A0A1D6I8X8 View 3D Structure Click here
A0A1D6JPE7 View 3D Structure Click here
A0A1D6JVU0 View 3D Structure Click here
A0A1D6K4K4 View 3D Structure Click here
A0A1D6KC44 View 3D Structure Click here
A0A1D6KIJ0 View 3D Structure Click here
A0A1D6KJX9 View 3D Structure Click here
A0A1D6MD71 View 3D Structure Click here
A0A1D6MDJ1 View 3D Structure Click here
A0A1D6NNW3 View 3D Structure Click here
A0A1D6NY61 View 3D Structure Click here
A0A1D6PIV5 View 3D Structure Click here
A0A1D6PIV5 View 3D Structure Click here
A0A1D6PR89 View 3D Structure Click here
B4F9Z5 View 3D Structure Click here
B4FKZ5 View 3D Structure Click here
B4FQN3 View 3D Structure Click here
B4FQV8 View 3D Structure Click here
B4G098 View 3D Structure Click here
B4G0N2 View 3D Structure Click here
B6T9X3 View 3D Structure Click here
B7F5B4 View 3D Structure Click here
B8A0R6 View 3D Structure Click here
C0HFG8 View 3D Structure Click here
C0P6F4 View 3D Structure Click here
C4J6K8 View 3D Structure Click here
I1JB48 View 3D Structure Click here
I1JS32 View 3D Structure Click here
I1JU36 View 3D Structure Click here
I1JW76 View 3D Structure Click here
I1K1C8 View 3D Structure Click here
I1K220 View 3D Structure Click here
I1K772 View 3D Structure Click here
I1K8I9 View 3D Structure Click here
I1KDA1 View 3D Structure Click here
I1KWU8 View 3D Structure Click here
I1L7C8 View 3D Structure Click here
I1LC39 View 3D Structure Click here
I1LFE3 View 3D Structure Click here
I1LR32 View 3D Structure Click here
I1M4R4 View 3D Structure Click here
I1M8B7 View 3D Structure Click here
I1MDK4 View 3D Structure Click here
I1MEJ6 View 3D Structure Click here
I1MGM6 View 3D Structure Click here
I1MUD9 View 3D Structure Click here
I1MW41 View 3D Structure Click here
I1MXW6 View 3D Structure Click here
I1NFI7 View 3D Structure Click here
I1NIB0 View 3D Structure Click here
K7KAZ2 View 3D Structure Click here
K7LBS0 View 3D Structure Click here
K7LL62 View 3D Structure Click here
K7LPR9 View 3D Structure Click here
K7M1J7 View 3D Structure Click here
K7M9M3 View 3D Structure Click here
K7N3L0 View 3D Structure Click here
K7VAF4 View 3D Structure Click here
K7VFS7 View 3D Structure Click here
K7VKG9 View 3D Structure Click here
K7VSC9 View 3D Structure Click here
K7VT98 View 3D Structure Click here
O48780 View 3D Structure Click here
O65677 View 3D Structure Click here
Q0DUX1 View 3D Structure Click here
Q0IRW8 View 3D Structure Click here
Q10KI1 View 3D Structure Click here
Q10P61 View 3D Structure Click here
Q10PV5 View 3D Structure Click here
Q10QW1 View 3D Structure Click here
Q38860 View 3D Structure Click here
Q4V3C9 View 3D Structure Click here
Q570B4 View 3D Structure Click here
Q5XEP9 View 3D Structure Click here
Q5Z6S3 View 3D Structure Click here
Q688V9 View 3D Structure Click here
Q69X62 View 3D Structure Click here
Q6F365 View 3D Structure Click here
Q6K3E6 View 3D Structure Click here
Q6K558 View 3D Structure Click here
Q6TMJ4 View 3D Structure Click here
Q6Z6C7 View 3D Structure Click here
Q75M74 View 3D Structure Click here
Q7XEM4 View 3D Structure Click here
Q8LQT7 View 3D Structure Click here
Q9C6L5 View 3D Structure Click here
Q9C992 View 3D Structure Click here
Q9FG87 View 3D Structure Click here
Q9FH27 View 3D Structure Click here
Q9FW59 View 3D Structure Click here
Q9LN49 View 3D Structure Click here
Q9LQP8 View 3D Structure Click here
Q9LZ72 View 3D Structure Click here
Q9MAM3 View 3D Structure Click here
Q9SIB2 View 3D Structure Click here
Q9SIX1 View 3D Structure Click here
Q9SS39 View 3D Structure Click here
Q9SUY9 View 3D Structure Click here
Q9SYZ0 View 3D Structure Click here
Q9XF43 View 3D Structure Click here
Q9ZUZ0 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;