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0  structures 385  species 0  interactions 614  sequences 1  architecture

Family: ComK (PF06338)

Summary: ComK protein

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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


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. 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].

Gene Ontology

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

Domain organisation

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Pfam Clan

This family is a member of clan PLP_aminotran (CL0061), which has the following description:

This superfamily contains a variety of PLP-dependent enzymes.

The clan contains the following 16 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Aminotran_MocR Beta_elim_lyase ComK Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SepSecS SHMT

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.

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  Seed
(20)
Full
(614)
Representative proteomes UniProt
(2316)
NCBI
(3387)
Meta
(0)
RP15
(122)
RP35
(414)
RP55
(612)
RP75
(922)
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  Seed
(20)
Full
(614)
Representative proteomes UniProt
(2316)
NCBI
(3387)
Meta
(0)
RP15
(122)
RP35
(414)
RP55
(612)
RP75
(922)
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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.