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0  structures 809  species 0  interactions 904  sequences 3  architectures

Family: EII-GUT (PF03608)

Summary: PTS system enzyme II sorbitol-specific factor

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PTS system enzyme II sorbitol-specific factor Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004699

Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.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 Gut family consists only of glucitol-specific transporters, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli consists of IIA protein, a IIC protein and a IIBC protein.

    This family is specific for the IIC component.

    Gene Ontology

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    Domain organisation

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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
    (17)
    Full
    (904)
    Representative proteomes NCBI
    (276)
    Meta
    (63)
    RP15
    (22)
    RP35
    (38)
    RP55
    (61)
    RP75
    (76)
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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
    (17)
    Full
    (904)
    Representative proteomes NCBI
    (276)
    Meta
    (63)
    RP15
    (22)
    RP35
    (38)
    RP55
    (61)
    RP75
    (76)
    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
    (17)
    Full
    (904)
    Representative proteomes NCBI
    (276)
    Meta
    (63)
    RP15
    (22)
    RP35
    (38)
    RP55
    (61)
    RP75
    (76)
    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: 17
    Number in full: 904
    Average length of the domain: 163.20 aa
    Average identity of full alignment: 64 %
    Average coverage of the sequence by the domain: 89.76 %

    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 25.0 25.0
    Trusted cut-off 26.9 26.7
    Noise cut-off 22.5 22.3
    Model length: 168
    Family (HMM) version: 8
    Download: download the raw HMM for this family

    Species distribution

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