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0  structures 1701  species 0  interactions 1762  sequences 9  architectures

Family: SfsA (PF03749)

Summary: Sugar fermentation stimulation protein

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.

Sugar fermentation stimulation protein Provide feedback

This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA [2] and it contains a helix-turn-helix motif that probably binds DNA at its C-terminus.

Literature references

  1. Kawamukai M, Utsumi R, Takeda K, Higashi A, Matsuda H, Choi YL, Komano T; , J Bacteriol 1991;173:2644-2648.: Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli. PUBMED:2013578 EPMC:2013578

  2. Takeda K, Akimoto C, Kawamukai M; , Biosci Biotechnol Biochem 2001;65:213-217.: Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA. PUBMED:11272834 EPMC:11272834


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005224

The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [PUBMED:2013578].

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
(13)
Full
(1762)
Representative proteomes NCBI
(1213)
Meta
(1569)
RP15
(139)
RP35
(263)
RP55
(348)
RP75
(410)
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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
(13)
Full
(1762)
Representative proteomes NCBI
(1213)
Meta
(1569)
RP15
(139)
RP35
(263)
RP55
(348)
RP75
(410)
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
(13)
Full
(1762)
Representative proteomes NCBI
(1213)
Meta
(1569)
RP15
(139)
RP35
(263)
RP55
(348)
RP75
(410)
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: COG1489
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 13
Number in full: 1762
Average length of the domain: 211.30 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 87.65 %

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 29.7 26.6
Noise cut-off 23.8 24.6
Model length: 216
Family (HMM) version: 8
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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