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. The family also includes proteins which are involved in the binding/transport of lipids.
Internal database links
|SCOOP:||COXG AHSA1 DUF1857 Polyketide_cyc2 DUF2505|
|Similarity to PfamA using HHSearch:||COXG Polyketide_cyc2|
This tab holds annotation information from the InterPro database.
InterPro entry IPR005031
This entry represents the START domain found in polyketide cylcases/dehydrases such as TcmN [PUBMED:1548230] and in coenzyme Q-binding protein COQ10 [PUBMED:19120452]. COQ10 is required for the function of coenzyme Q in the respiratory chain and has a steroidogenic acute regulatory protein-related lipid transfer (START) domain, known to bind specific lipids in other START domain family members [PUBMED:23270816, PUBMED:11276083].
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This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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The Bet_V_I family is composed of sequences related to the major Birch (Betula verrucose) pollen antigen Betv1. This allergen is known to cause hayfever, dermatitis, asthma and occasionally anaphylactic shock. The other families in this clan share the same structure as Betv1 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  which seems a common feature of the families in this clan.
The clan contains the following 14 members:AHSA1 Aromatic_hydrox Bet_v_1 COXG DUF1857 DUF2505 DUF3074 DUF3211 DUF3284 IP_trans Polyketide_cyc Polyketide_cyc2 Ring_hydroxyl_A START
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Seed source:||Pfam-B_1457 (release 6.6)|
|Author:||Mifsud W, Mistry J, Wood V|
|Number in seed:||95|
|Number in full:||2766|
|Average length of the domain:||129.50 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||60.23 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_cyc domain has been found. There are 31 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 seqence.
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