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0  structures 864  species 0  interactions 1174  sequences 2  architectures

Family: AbrB (PF05145)

Summary: Transition state regulatory protein AbrB

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Transition state regulatory protein AbrB Provide feedback

Bacillus subtilis respond to a multitude of environmental stimuli by using transcription factors called transition state regulators (TSRs). They play an essential role in cell survival by regulating spore formation, competence, and biofilm development. AbrB is one of the most known TSRs, acting as a pleotropic regulator for over 60 different genes where it directly binds to their promoter or regulatory regions. Many other genes are indirectly controlled by AbrB since it is a regulator of other regulatory proteins, including ScoC, Abh, SinR and SigH [1]. Hence, AbrB is considered a global regulatory protein controlling processes such as Bacillus subtilis growth and cell division as well as production of extracellular degradative enzymes, nitrogen utilization and amino acid metabolism, motility, synthesis of antibiotics and their resistant determinants, development of competence, transport systems, oxidative stress response, phosphate metabolism, cell surface components and sporulation [2]. AbrB is a tetramer consisting of identical 94 residue monomers. Its DNA-binding function resides solely in the N-terminal domain (AbrBN) of 53 residues [3]. Although it does not recognize a well-defined DNA base-pairing sequence, instead, it appears to target a very weak pseudo consensus nucleotide sequence, TGGNA-5bp-TGGNA, which allows it to be rather promiscuous in binding [1]. The N-terminal domains of very similar sequences are present in two more Bacillus subtilis proteins, Abh and SpoVT. Mutagenesis studies suggest that the role of the C-terminal domain is in forming multimers [4].

Literature references

  1. Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance M, Strauch MA, Cavanagh J;, Structure. 2008;16:1702-1713.: Insights into the nature of DNA binding of AbrB-like transcription factors. PUBMED:19000822 EPMC:19000822

  2. Phillips ZE, Strauch MA;, Cell Mol Life Sci. 2002;59:392-402.: Bacillus subtilis sporulation and stationary phase gene expression. PUBMED:11964117 EPMC:11964117

  3. Vaughn JL, Feher V, Naylor S, Strauch MA, Cavanagh J;, Nat Struct Biol. 2000;7:1139-1146.: Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator abrB. PUBMED:11101897 EPMC:11101897

  4. Bobay BG, Andreeva A, Mueller GA, Cavanagh J, Murzin AG;, FEBS Lett. 2005;579:5669-5674.: Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. PUBMED:16223496 EPMC:16223496


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007820

AbrB is a multipass membrane protein [PUBMED:15919996] that is involved in the regulation of alkylation damage induced protein AidB in Escherichia coli [PUBMED:8002588].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Membrane_trans (CL0142), which has the following description:

This clan contains membrane proteins involved in the transport of molecules including amino acids sugars and signalling molecules. It also includes integral membrane cell cycle proteins and some putative ammonia monooxygenases.

The clan contains the following 7 members:

ABC-3 AbrB BPD_transp_2 DUF1275 FecCD FTSW_RODA_SPOVE Pam17

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(148)
Full
(1174)
Representative proteomes UniProt
(3964)
NCBI
(7739)
Meta
(1250)
RP15
(122)
RP35
(628)
RP55
(1227)
RP75
(2050)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(148)
Full
(1174)
Representative proteomes UniProt
(3964)
NCBI
(7739)
Meta
(1250)
RP15
(122)
RP35
(628)
RP55
(1227)
RP75
(2050)
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
(148)
Full
(1174)
Representative proteomes UniProt
(3964)
NCBI
(7739)
Meta
(1250)
RP15
(122)
RP35
(628)
RP55
(1227)
RP75
(2050)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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.

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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: COG3180
Previous IDs: AmoA;
Type: Family
Author: Bateman A
Number in seed: 148
Number in full: 1174
Average length of the domain: 281.80 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 89.71 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.1 27.1
Trusted cut-off 27.6 27.5
Noise cut-off 27.0 26.7
Model length: 314
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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