Summary: Polyketide cyclase / dehydrase and lipid transport
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Polyketide cyclase / dehydrase and lipid transport Provide feedback
This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily [1].
Literature references
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Iyer LM, Koonin EV, Aravind L; , Proteins. 2001;43:134-144.: Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. PUBMED:11276083 EPMC:11276083
Internal database links
SCOOP: | AHSA1 Bet_v_1 COXG DUF1857 DUF2505 DUF2867 DUF3284 Polyketide_cyc START |
Similarity to PfamA using HHSearch: | Bet_v_1 Polyketide_cyc COXG AHSA1 DUF2505 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019587
This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily [PUBMED:11276083].
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 Bet_v_1_like (CL0209), which has the following description:
The Pfam:PF00407 entry is composed of sequences related to the major Birch (Betula verrucose) pollen antigen Bet v 1. This allergen is known to cause hayfever, dermatitis, asthma and occasionally anaphylactic shock. The other families in this clan share the same structure as Bet v 1, which is composed of antiparallel beta sheets and alpha helices. There is a cavity between the beta sheet and a long C terminal helix. The cavity appears to play roles in the binding of lipid molecules [1][2][3] which seems a common feature of the families in this clan.
The clan contains the following 21 members:
AHSA1 Aromatic_hydrox Bet_v_1 COXG DAPG_hydrolase DUF1857 DUF2505 DUF3074 DUF3211 DUF3284 Fungal_KA1 IP_trans Lipoprotein_18 PaO Polyketide_cyc Polyketide_cyc2 PRELI Ring_hydroxyl_A START VanA_C VAStAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (114) |
Full (15309) |
Representative proteomes | UniProt (55354) |
NCBI (120583) |
Meta (1043) |
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RP15 (1066) |
RP35 (6076) |
RP55 (15171) |
RP75 (27656) |
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Jalview | |||||||||
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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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 (114) |
Full (15309) |
Representative proteomes | UniProt (55354) |
NCBI (120583) |
Meta (1043) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1066) |
RP35 (6076) |
RP55 (15171) |
RP75 (27656) |
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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: | Manual |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Iyer LM |
Number in seed: | 114 |
Number in full: | 15309 |
Average length of the domain: | 143.30 aa |
Average identity of full alignment: | 14 % |
Average coverage of the sequence by the domain: | 81.97 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 144 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
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 Polyketide_cyc2 domain has been found. There are 143 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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