Summary: Phenylacetic acid catabolic protein
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Phenylacetic acid catabolic protein Provide feedback
This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid . These proteins may form part of a dioxygenase complex.
Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E; , J Biol Chem 1998;273:25974-25986.: Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. PUBMED:9748275 EPMC:9748275
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The members of this clan all share a distinctive four helical bundle. The four helices are arranged antiparallel with a left-handed twist. This helical bundle is distinguished from others by the long connection between the second and third helices. Some of the members contain a Fe or Mn dimer at the centre of the helical bundle. The ferritin fold was first described by Murzin AG and Chothia C, Cur Opin Struc Biol 1992, 2:895-903.
The clan contains the following 19 members:Coat_F COQ7 DUF2202 DUF2383 DUF305 DUF4142 DUF4439 DUF892 FA_desaturase_2 Ferritin Ferritin-like Ferritin_2 MiaE MiaE_2 Mn_catalase PaaA_PaaC Phenol_Hydrox Ribonuc_red_sm Rubrerythrin
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||117|
|Number in full:||1413|
|Average length of the domain:||266.20 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||88.22 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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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 PaaA_PaaC domain has been found. There are 42 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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