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24  structures 2192  species 1  interaction 4169  sequences 31  architectures

Family: DUF59 (PF01883)

Summary: Domain of unknown function DUF59

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.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

Domain of unknown function DUF59 Provide feedback

This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine [1]. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) O84984 from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF) O84982 PaaI (PhaG) O84983 and PaaK (PhaI) O84985 which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid [2]. It also includes PaaD P76080 from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation [3]. It is found near the N-terminus of the chloroplast scaffold protein HCF101 Q8LD16 involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins [4].

Literature references

  1. Almeida MS, Herrmann T, Peti W, Wilson IA, Wuthrich K;, Protein Sci. 2005;14:2880-2886.: NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins. PUBMED:16199668 EPMC:16199668

  2. Olivera ER, Minambres B, Garcia B, Muniz C, Moreno MA, Ferrandez A, Diaz E, Garcia JL, Luengo JM; , Proc Natl Acad Sci U S A 1998;95:6419-6424.: Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon. PUBMED:9600981 EPMC:9600981

  3. 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

  4. Schwenkert S, Netz DJ, Frazzon J, Pierik AJ, Bill E, Gross J, Lill R, Meurer J;, Biochem J. 2009;425:207-214.: Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly. PUBMED:19817716 EPMC:19817716


This tab holds annotation information from the InterPro database.

InterPro entry IPR002744

This family includes prokaryotic proteins of unknown function. The family also includes PhaH (SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (SWISSPROT), PhaG (SWISSPROT) and PhaI (SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid [PUBMED:9600981]. So members of this family may all be components of ring hydroxylating complexes.

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 NifU (CL0232), which has the following description:

This clan includes the C-terminal domain of NifU as well as a large family of uncharacterised domains.

The clan contains the following 2 members:

DUF59 NifU

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, 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
(43)
Full
(4169)
Representative proteomes UniProt
(16056)
NCBI
(20500)
Meta
(2563)
RP15
(1023)
RP35
(3041)
RP55
(5596)
RP75
(8653)
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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
(43)
Full
(4169)
Representative proteomes UniProt
(16056)
NCBI
(20500)
Meta
(2563)
RP15
(1023)
RP35
(3041)
RP55
(5596)
RP75
(8653)
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
(43)
Full
(4169)
Representative proteomes UniProt
(16056)
NCBI
(20500)
Meta
(2563)
RP15
(1023)
RP35
(3041)
RP55
(5596)
RP75
(8653)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Enright A
Previous IDs: none
Type: Family
Author: Enright A, Ouzounis C, Bateman A, Eberhardt R
Number in seed: 43
Number in full: 4169
Average length of the domain: 74.80 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 32.39 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 74
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There is 1 interaction for this family. More...

DUF59

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 DUF59 domain has been found. There are 24 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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