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0  structures 1165  species 0  interactions 1205  sequences 3  architectures

Family: HemX (PF04375)

Summary: HemX

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.

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.

HemX Provide feedback

This family consists of several bacterial HemX proteins. The hemX gene is not essential for haem synthesis in B. subtilis. HemX is a polytopic membrane protein which by an unknown mechanism down-regulates the level of HemA [1].

Literature references

  1. Johansson P, Hederstedt L; , Microbiology 1999;145:529-538.: Organization of genes for tetrapyrrole biosynthesis in gram--positive bacteria. PUBMED:10217486 EPMC:10217486


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007470

The majority of proteins in this family are annotated as uroporphyrin-III C-methyltransferase (EC) [PUBMED:3062586]; however, there is no direct evidence to support this annotation for these proteins, which come from mainly pathogenic Gram-negative organisms. There is some evidence to suggest that the proteins are membrane anchored as they have a predicted N-terminal signal peptide and transmembrane domain and may be involved in haem transport [PUBMED:9006036].

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 EpsM (CL0331), which has the following description:

These families are involved in the general secretory pathways of bacteria and are normally membrane-bound.

The clan contains the following 8 members:

DUF2514 GspL_C HemX Phage_lysis PilN PilO T2SM T2SM_b

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
(5)
Full
(1205)
Representative proteomes NCBI
(918)
Meta
(162)
RP15
(34)
RP35
(94)
RP55
(156)
RP75
(207)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(5)
Full
(1205)
Representative proteomes NCBI
(918)
Meta
(162)
RP15
(34)
RP35
(94)
RP55
(156)
RP75
(207)
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
(5)
Full
(1205)
Representative proteomes NCBI
(918)
Meta
(162)
RP15
(34)
RP35
(94)
RP55
(156)
RP75
(207)
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.

Pfam alignments:

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: COG2959
Previous IDs: DUF513;
Type: Family
Author: Kerrison ND, Moxon SJ
Number in seed: 5
Number in full: 1205
Average length of the domain: 356.10 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 87.20 %

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 29.3 29.3
Trusted cut-off 29.5 29.3
Noise cut-off 29.2 29.2
Model length: 372
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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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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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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