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26  structures 2274  species 0  interactions 6066  sequences 24  architectures

Family: GyrI-like (PF06445)

Summary: GyrI-like small molecule binding domain

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GyrI-like small molecule binding domain Provide feedback

This family contains the small molecule binding domain of a number of different bacterial transcription activators [1]. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding [3]. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira [3].

Literature references

  1. Kwon HJ, Bennik MH, Demple B, Ellenberger T; , Nat Struct Biol 2000;7:424-430.: Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. PUBMED:10802742 EPMC:10802742

  2. Romanowski MJ, Gibney SA, Burley SK; , Proteins 2002;47:403-407.: Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17. PUBMED:11948793 EPMC:11948793

  3. Anantharaman V, Aravind L;, Proteins. 2004;56:795-807.: The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. PUBMED:15281131 EPMC:15281131


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010499

This domain is found in the probable effector binding domain of a number of different bacterial transcription activators [PUBMED:10802742] and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.

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 SHS2 (CL0319), which has the following description:

SHS2 is a novel domain with a simple fold containing a core of 3 strands, forming a curved sheet, and a single helix in a strand-helix-strand-strand (SHS2) configuration [1]. SHS2 is found in the bacterial cell division ATPase FtsA, the archaeo-eukaryotic RNA polymerase subunit Rpb7p, the GyrI superfamily, and the uncharacterized MTH1598/Tm1083-like proteins [1]. The fold exists as single copy versions in FtsA (where it is inserted into the RNAseH fold), Rbp7p and Dodecin [1]. It is found as a diad in the GyrI superfamily. In MTH1598/Tm1083-like proteins two copies of SHS2 are found with one inserted into another [1]. The single-copy versions in FtsA and Rbp7 mediate protein–protein interactions, while the one in Dodecin is a small molecule binding domain. The GyrI also binds small molecule, while the MTH1598 is predicted to be enzymatic [1].

The clan contains the following 7 members:

Archease Cass2 Dodecin GyrI-like SHS2_FTSA SHS2_Rpb7-N SOUL

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
(88)
Full
(6066)
Representative proteomes NCBI
(4279)
Meta
(124)
RP15
(387)
RP35
(718)
RP55
(907)
RP75
(1074)
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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
(88)
Full
(6066)
Representative proteomes NCBI
(4279)
Meta
(124)
RP15
(387)
RP35
(718)
RP55
(907)
RP75
(1074)
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
(88)
Full
(6066)
Representative proteomes NCBI
(4279)
Meta
(124)
RP15
(387)
RP35
(718)
RP55
(907)
RP75
(1074)
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: Pfam-B_36124 (release 9.0)
Previous IDs: AraC_E_bind;
Type: Domain
Author: Finn RD, Anantharaman V
Number in seed: 88
Number in full: 6066
Average length of the domain: 155.40 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 64.70 %

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 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 155
Family (HMM) version: 10
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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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 GyrI-like domain has been found. There are 26 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.

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