Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
39  structures 2718  species 1  interaction 8406  sequences 38  architectures

Family: EIIA-man (PF03610)

Summary: PTS system fructose IIA component

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.

PTS system fructose IIA component Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004701

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [PUBMED:8246840, PUBMED:2197982] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.

The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC [PUBMED:1537788]. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).

The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.

An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [PUBMED:8246840, PUBMED:1537788, PUBMED:7815935, PUBMED:11361063].

The Man family is unique in several respects among PTS permease families.

  • It is the only PTS family in which members possess a IID protein.
  • It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.
  • Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.
  • The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine.

    This family is specific for IIA and IIB components.

    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...

    Loading domain graphics...

    Pfam Clan

    This family is a member of clan EDD (CL0245), which contains the following 4 members:

    Dak1 Dak1_2 DegV EIIA-man

    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
    (36)
    Full
    (8406)
    Representative proteomes NCBI
    (3993)
    Meta
    (258)
    RP15
    (255)
    RP35
    (550)
    RP55
    (740)
    RP75
    (912)
    Jalview View  View  View  View  View  View  View  View 
    HTML View    View  View  View  View     
    PP/heatmap 1   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
    (36)
    Full
    (8406)
    Representative proteomes NCBI
    (3993)
    Meta
    (258)
    RP15
    (255)
    RP35
    (550)
    RP55
    (740)
    RP75
    (912)
    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
    (36)
    Full
    (8406)
    Representative proteomes NCBI
    (3993)
    Meta
    (258)
    RP15
    (255)
    RP35
    (550)
    RP55
    (740)
    RP75
    (912)
    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: TIGRFAMs
    Previous IDs: none
    Type: Family
    Author: TIGRFAMs, Griffiths-Jones SR
    Number in seed: 36
    Number in full: 8406
    Average length of the domain: 113.60 aa
    Average identity of full alignment: 21 %
    Average coverage of the sequence by the domain: 41.09 %

    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 21.0 21.0
    Trusted cut-off 21.0 21.2
    Noise cut-off 20.9 20.9
    Model length: 116
    Family (HMM) version: 11
    Download: download the raw HMM for this family

    Species distribution

    Sunburst controls

    Show

    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...

    Loading sunburst data...

    Tree controls

    Hide

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

    Loading...

    Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

    Interactions

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

    EIIA-man

    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 EIIA-man domain has been found. There are 39 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.

    Loading structure mapping...