Summary

Bacterial regulatory proteins, gntR family

This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR [4]. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships [3]. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor [5].

Literature references

Lee MH, Scherer M, Rigali S, Golden JW; , J Bacteriol 2003;185:4315-4325.: PlmA, a new member of the GntR family, has plasmid maintenance functions in Anabaena sp. strain PCC 7120. PUBMED:12867439
Rigali S, Derouaux A, Giannotta F, Dusart J; , J Biol Chem 2002;277:12507-12515.: Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. PUBMED:11756427
Rigali S, Schlicht M, Hoskisson P, Nothaft H, Merzbacher M, Joris B, Titgemeyer F; , Nucleic Acids Res 2004;32:3418-3426.: Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships. PUBMED:15247334
Hillerich B, Westpheling J; , J Bacteriol. 2006;188:7477-7487.: A new GntR family transcriptional regulator in streptomyces coelicolor is required for morphogenesis and antibiotic production and controls transcription of an ABC transporter in response to carbon source. PUBMED:16936034
Rigali S, Nothaft H, Noens EE, Schlicht M, Colson S, Muller M, Joris B, Koerten HK, Hopwood DA, Titgemeyer F, van Wezel GP; , Mol Microbiol. 2006;61:1237-1251.: The sugar phosphotransferase system of Streptomyces coelicolor is regulated by the GntR-family regulator DasR and links N-acetylglucosamine metabolism to the control of development. PUBMED:16925557
Gorelik M, Lunin VV, Skarina T, Savchenko A; , Protein Sci. 2006;15:1506-1511.: Structural characterization of GntR/HutC family signaling domain. PUBMED:16672238

InterPro entry IPR000524

Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon PUBMED:2060763. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined PUBMED:11013219. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies PUBMED:11756427. This entry represents the N-terminal DNA-binding domain of the GntR family.

Clan

This family is a member of clan HTH (CL0123), which contains the following 141 members:

Arg_repressor B-block_TFIIIC Bac_DnaA_C BetR BrkDBD CENP-B_N Coprinus_mating Cro Crp DDRGK Dimerisation DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF2089 DUF2250 DUF2316 DUF293 DUF3116 DUF387 DUF739 DUF742 DUF977 E2F_TDP ELK Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC Ftsk_gamma FUR GcrA GerE GntR Homeobox Homez HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_14 HTH_15 HTH_3 HTH_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_CodY HTH_DeoR HTH_IclR HTH_Mga HTH_psq HTH_WhiA HxlR IF2_N Ins_element1 KorB LacI LexA_DNA_bind MarR Med9 MerR MerR-DNA-bind Mga Mnd1 Mor MotA_activ Mu_DNA_bind Myb_DNA-bind_2 Myb_DNA-binding NUMOD1 PaaX PadR PAX PCI PCI_Csn8 Pencillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL RFX_DNA_binding Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP SAC3_GANP Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SpoIIID Sulfolobus_pRN TBPIP Tc3_transposase Terminase_5 TetR_N TFIIE_alpha Trans_reg_C Transposase_14 Transposase_5 Transposase_8 Transposase_Tc5 TrfA TrmB Trp_repressor UPF0122 z-alpha

Gene Ontology

Cellular component	intracellular (GO:0005622)
Molecular function	transcription factor activity (GO:0003700)
Biological process	regulation of transcription, DNA-dependent (GO:0006355)

External database links

PANDIT:	PF00392
PROSITE:	PDOC00042
SCOP:	1e2x
SYSTERS:	GntR

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

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (27) Full (17532) NCBI (15132) Metagenomics (2844)
Viewer:

Formatting options

Alignment:	Seed (27) Full (17532)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (27) Full (17532) NCBI (15132) Metagenomics (2844)
Full length sequences	Full-sequences (17532)

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 HMMER2.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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

Seed source:

Prosite & Pfam-B_6405 (Release 8.0)

Previous IDs:

gntR;

Type:

Family

Author:

Finn RD, Bateman A, Hoskisson PA

Number in seed:

27

Number in full:

17532

Average length of the domain:

62.80 aa

Average identity of full alignment:

29 %

Average coverage of the sequence by the domain:

22.14 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	21.4	21.4
Trusted cut-off	21.4	21.4
Noise cut-off	21.3	21.3

Model length:

64

Family (HMM) version:

14

Download:

download the raw HMM for this family

Species distribution

Tree controls

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

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

There are 3 interactions for this family. More...

GntR FadR_C FCD

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 GntR domain has been found.

Loading structure mapping...

Family: GntR (PF00392)

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