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1  structure 2547  species 0  interactions 3245  sequences 11  architectures

Family: RskA (PF10099)

Summary: Anti-sigma-K factor rskA

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Anti-sigma-K factor rskA Provide feedback

This domain, formerly known as DUF2337, is the anti-sigma-K factor, RskA. In Mycobacterium tuberculosis the protein positively regulates expression of the antigenic proteins MPB70 and MPB83 [1].

Literature references

  1. Said-Salim B, Mostowy S, Kristof AS, Behr MA; , Mol Microbiol. 2006;62:1251-1263.: Mutations in Mycobacterium tuberculosis Rv0444c, the gene encoding anti-SigK, explain high level expression of MPB70 and MPB83 in Mycobacterium bovis. PUBMED:17064366 EPMC:17064366


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018764

RskA (regulator of sigma K) represses the extra-cytoplasmic function (ECF) sigma factor K (sigK) by binding to it and inhibiting its activity [PUBMED:18203833]. This leads to a decreased expression of SigK-regulated genes, such as mpt70 and mpt83. RskA is found in various Mycobacterium, such as Mycobacterium tuberculosis. However, in Mycobacterium bovis it is probably dysfunctional, due to at least one of the two natural occurring polymorphisms in its encoding gene, when compared to M. tuberculosis [PUBMED:17064366]. This leads to an increased expression of SigK-regulated genes.

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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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...

View options

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
(231)
Full
(3245)
Representative proteomes UniProt
(7820)
NCBI
(11569)
Meta
(70)
RP15
(530)
RP35
(1997)
RP55
(3322)
RP75
(4783)
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HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(231)
Full
(3245)
Representative proteomes UniProt
(7820)
NCBI
(11569)
Meta
(70)
RP15
(530)
RP35
(1997)
RP55
(3322)
RP75
(4783)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(231)
Full
(3245)
Representative proteomes UniProt
(7820)
NCBI
(11569)
Meta
(70)
RP15
(530)
RP35
(1997)
RP55
(3322)
RP75
(4783)
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.

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: COGs (COG5343)
Previous IDs: DUF2337;
Type: Family
Sequence Ontology: SO:0100021
Author: COGs, Finn RD , Sammut SJ
Number in seed: 231
Number in full: 3245
Average length of the domain: 191.60 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 75.45 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 35.2 35.2
Trusted cut-off 35.2 35.2
Noise cut-off 35.1 35.1
Model length: 180
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 RskA domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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