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0  structures 4131  species 0  interactions 4251  sequences 14  architectures

Family: Competence (PF03772)

Summary: Competence protein

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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.

Competence protein Provide feedback

Members of this family are integral membrane proteins with 6 predicted transmembrane helices. Some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA [1,4]. These proteins may transport DNA across the cell membrane. These proteins contain a highly conserved motif in the amino terminal transmembrane region that has two histidines that may form a metal binding site.

Literature references

  1. Facius D, Meyer TF; , Mol Microbiol 1993;10:699-712.: A novel determinant (comA) essential for natural transformation competence in Neisseria gonorrhoeae and the effect of a comA defect on pilin variation. PUBMED:7934834 EPMC:7934834

  2. Hahn J, Inamine G, Kozlov Y, Dubnau D; , Mol Microbiol 1993;10:99-111.: Characterization of comE, a late competence operon of Bacillus subtilis required for the binding and uptake of transforming DNA. PUBMED:7968523 EPMC:7968523

  3. Clifton SW, McCarthy D, Roe BA; , Gene 1994;146:95-100.: Sequence of the rec-2 locus of Haemophilus influenzae: homologies to comE-ORF3 of Bacillus subtilis and msbA of Escherichia coli. PUBMED:8063112 EPMC:8063112

  4. Pestova EV, Morrison DA; , J Bacteriol 1998;180:2701-2710.: Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector. PUBMED:9573156 EPMC:9573156


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004477

This family is defined to identify a pair of paralogous 3' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterised originally as required for the expression of virulence genes, but is now recognised as the exoribonuclease RNase R (Rnr). Its paralog in Escherichia coli and Haemophilus influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cut off to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3' exoribonucleases.

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget [PUBMED:11483988]. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible.

DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions [PUBMED:8901420].

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
(123)
Full
(4251)
Representative proteomes NCBI
(3604)
Meta
(477)
RP15
(309)
RP35
(604)
RP55
(770)
RP75
(907)
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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
(123)
Full
(4251)
Representative proteomes NCBI
(3604)
Meta
(477)
RP15
(309)
RP35
(604)
RP55
(770)
RP75
(907)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(123)
Full
(4251)
Representative proteomes NCBI
(3604)
Meta
(477)
RP15
(309)
RP35
(604)
RP55
(770)
RP75
(907)
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: COG0658
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 123
Number in full: 4251
Average length of the domain: 262.70 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 39.09 %

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 20.2 20.2
Trusted cut-off 20.3 20.6
Noise cut-off 20.1 20.1
Model length: 271
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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