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3  structures 1339  species 0  interactions 1349  sequences 4  architectures

Family: Iron_traffic (PF04362)

Summary: Bacterial Fe(2+) trafficking

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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.

Bacterial Fe(2+) trafficking Provide feedback

This is a family of bacterial Fe(2+) trafficking proteins.

Literature references

  1. Wasinger VC, Humphery-Smith I; , FEMS Microbiol Lett 1998;169:375-382.: Small genes/gene-products in Escherichia coli K-12. PUBMED:9868784 EPMC:9868784

  2. Link AJ, Robison K, Church GM; , Electrophoresis 1997;18:1259-1313.: Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. PUBMED:9298646 EPMC:9298646

  3. Osborne MJ, Siddiqui N, Landgraf D, Pomposiello PJ, Gehring K; , Protein Sci 2005;14:1673-1678.: The solution structure of the oxidative stress-related protein YggX from Escherichia coli. PUBMED:15883188 EPMC:15883188


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007457

The protein represented by this entry, YggX, serves to protect Fe-S clusters from oxidative damage [PUBMED:11416172]. The effect is two-fold: proteins that rely on Fe-S clusters do not become inactivated, and the release of free iron and hydrogen peroxide--a DNA damaging agent--is prevented. These observations are consistent with the hypothesis that YggX chelates free iron, and recent experiments show that YggX can indeed bind Fe(II) in vitro and in vivo [PUBMED:12670952]. Furthermore, YggX has a positive effect on the action of at least one Fe(II)-responsive protein. The combined actions of YggX is reminiscent of iron trafficking proteins [PUBMED:12033438], and YggX is therefore proposed to play a role in Fe(II) trafficking [PUBMED:12670952]. In Escherichia coli, YggX was shown to be under the transcriptional control of the redox-sensing SoxRS system [PUBMED:14594836].

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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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(65)
Full
(1349)
Representative proteomes NCBI
(617)
Meta
(383)
RP15
(61)
RP35
(135)
RP55
(203)
RP75
(260)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(65)
Full
(1349)
Representative proteomes NCBI
(617)
Meta
(383)
RP15
(61)
RP35
(135)
RP55
(203)
RP75
(260)
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
(65)
Full
(1349)
Representative proteomes NCBI
(617)
Meta
(383)
RP15
(61)
RP35
(135)
RP55
(203)
RP75
(260)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: COG2924
Previous IDs: DUF495;
Type: Family
Author: Kerrison ND, Mistry J
Number in seed: 65
Number in full: 1349
Average length of the domain: 87.20 aa
Average identity of full alignment: 59 %
Average coverage of the sequence by the domain: 96.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 24.9 24.9
Noise cut-off 19.2 18.4
Model length: 88
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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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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 Iron_traffic domain has been found. There are 3 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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