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0  structures 443  species 0  interactions 719  sequences 2  architectures

Family: ComK (PF06338)

Summary: ComK 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.

ComK protein Provide feedback

This family consists of several bacterial ComK proteins. The ComK protein of Bacillus subtilis positively regulates the transcription of several late competence genes as well as comK itself. It has been found that ClpX plays an important role in the regulation of ComK at the post-transcriptional level [1].

Literature references

  1. Nanamiya H, Shiomi E, Ogura M, Tanaka T, Asai K, Kawamura F; , J Biochem (Tokyo) 2003;133:295-302.: Involvement of ClpX Protein in the Post-Transcriptional Regulation of a Competence Specific Transcription Factor, ComK Protein, of Bacillus subtilis. PUBMED:12761164 EPMC:12761164


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010461

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].

This family consists of several bacterial ComK proteins. ComK of Bacillus subtilis is a positive autoregulatory protein occupying a central position in the competence-signal-transduction network. It positively regulates the transcription of late competence genes, which specify morphogenetic and structural proteins necessary for construction of the DNA-binding and uptake apparatus, as well as the transcription of comK itself [PUBMED:12761164,PUBMED:7783616]. ComK specifically binds to the promoters of the genes that it affects. It has been found that ClpX plays an important role in the regulation of ComK at the post-transcriptional level [PUBMED:12761164].

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
(19)
Full
(719)
Representative proteomes NCBI
(336)
Meta
(0)
RP15
(15)
RP35
(32)
RP55
(49)
RP75
(58)
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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
(19)
Full
(719)
Representative proteomes NCBI
(336)
Meta
(0)
RP15
(15)
RP35
(32)
RP55
(49)
RP75
(58)
Alignment:
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Sequence:
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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
(19)
Full
(719)
Representative proteomes NCBI
(336)
Meta
(0)
RP15
(15)
RP35
(32)
RP55
(49)
RP75
(58)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
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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_13324 (release 9.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 19
Number in full: 719
Average length of the domain: 150.30 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 87.47 %

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 19.1 19.1
Trusted cut-off 19.1 19.3
Noise cut-off 18.7 18.8
Model length: 163
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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