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0  structures 822  species 0  interactions 859  sequences 1  architecture

Family: GutM (PF06923)

Summary: Glucitol operon activator protein (GutM)

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Glucitol operon activator protein (GutM) Provide feedback

This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes [1].

Literature references

  1. Yamada M, Saier MH Jr; , J Mol Biol 1988;203:569-583.: Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli. PUBMED:3062173 EPMC:3062173


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009693

This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system, which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes [PUBMED:3062173].

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...

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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
(26)
Full
(859)
Representative proteomes NCBI
(301)
Meta
(39)
RP15
(23)
RP35
(39)
RP55
(56)
RP75
(71)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(26)
Full
(859)
Representative proteomes NCBI
(301)
Meta
(39)
RP15
(23)
RP35
(39)
RP55
(56)
RP75
(71)
Alignment:
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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
(26)
Full
(859)
Representative proteomes NCBI
(301)
Meta
(39)
RP15
(23)
RP35
(39)
RP55
(56)
RP75
(71)
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

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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: Pfam-B_14714 (release 10.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 26
Number in full: 859
Average length of the domain: 109.20 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 81.79 %

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 30.2 29.9
Noise cut-off 19.4 19.0
Model length: 109
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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