Summary: Calcium-activated BK potassium channel alpha subunit

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Wikipedia: BK channel
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BK channel Edit Wikipedia article

KCNMA1
The domain structure of BK channels
Identifiers
Symbol	KCNMA1
Alt. symbols	SLO
Entrez	3778
HUGO	6284
OMIM	600150
RefSeq	NM_002247
UniProt	Q12791
Other data
Locus	Chr. 10 q22

KCNMB1
Identifiers
Symbol	KCNMB1
Entrez	3779
HUGO	6285
OMIM	603951
RefSeq	NM_004137
UniProt	Q16558
Other data
Locus	Chr. 5 q34

KCNMB2
Identifiers
Symbol	KCNMB2
Entrez	10242
HUGO	6286
OMIM	605214
RefSeq	NM_181361
UniProt	Q9Y691
Other data
Locus	Chr. 3 q26.32

KCNMB3
Identifiers
Symbol	KCNMB3
Alt. symbols	KCNMB2, KCNMBL
Entrez	27094
HUGO	6287
OMIM	605222
RefSeq	NM_171828
UniProt	Q9NPA1
Other data
Locus	Chr. 3 q26.3-q27

KCNMB3L
Identifiers
Symbol	KCNMB3L
Alt. symbols	KCNMB2L, KCNMBLP
Entrez	27093
HUGO	6288
RefSeq	NG_002679
Other data
Locus	Chr. 22 q11.1

KCNMB4
Identifiers
Symbol	KCNMB4
Entrez	27345
HUGO	6289
OMIM	605223
RefSeq	NM_014505
UniProt	Q86W47
Other data
Locus	Chr. 12 q15

Calcium-activated BK potassium channel alpha subunit

Identifiers

Symbol

BK_channel_a

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

BK channels (Big Potassium), also called Maxi-K or slo1, are potassium channels characterized by their large conductance of potassium ions (K⁺) through cell membranes. These channels are activated (opened) by changes in membrane electrical potential and/or by increases in concentration of intracellular calcium ion (Ca²⁺).^[1]^[2] Opening of BK channels allows K⁺ to passively flow through the channel, down the electrochemical gradient. Under typical physiological conditions, this results in an efflux of K⁺ from the cell, which leads to cell membrane hyperpolarization (an increase in the electrical potential across the cell membrane) and a decrease in cell excitability (a decrease in the probability that the cell will transmit an action potential).

BK channels are essential for the regulation of several key physiological processes including smooth muscle tone and neuronal excitability.^[3] They control the contraction of smooth muscle and are involved with the electrical tuning of hair cells in the cochlea. BK channels also contribute to the behavioral effects of ethanol in the worm C. elegans under high exogenous doses (> 100 mM) ^[4] that have been shown to correspond to biologically relevant internal ethanol concentrations.^[5] It remains to be determined if BK channels contribute to intoxication in humans.

Structure

As with most other voltage-gated potassium channels, BK channels have a tetrameric structure. Each monomer of the channel-forming alpha subunit is the product of the KCNMA1 gene. Modulatory beta subunits (encoded by KCNMB1, KCNMB2, KCNMB3, or KCNMB4) can associate with the tetrametic channel.

BK channels are a prime example of modular protein evolution. Each BK channel alpha subunit consists of (from N- to C-terminal):

A unique transmembrane domain (S0)^[6] that precedes the 6 transmembrane domains (S1-S6) conserved in all voltage-dependent K⁺ channels.
A voltage sensing domain (S1-S4).
A K⁺ channel pore domain (S5, selectivity filter, and S6).
A cytoplasmic C-terminal domain (CTD) consisting of a pair of RCK domains that assemble into an octameric gating ring on the intracellular side of the tetrameric channel.^[7]^[8]^[9]^[10]^[11] The CTD contains four primary binding sites for Ca²⁺, called "calcium bowls", encoded within the second RCK domain of each monomer.^[2]^[7]^[11]^[12]

Available X-ray structures:

3MT5 - Crystal Structure of the Human BK Gating Apparatus^[2]
3NAF - Structure of the Intracellular Gating Ring from the Human High-conductance Ca2+ gated K+ Channel (BK Channel)^[7]
3U6N - Open Structure of the BK channel Gating Ring^[12]

Pharmacology

BK channels are pharmacological targets for the treatment of several medical disorders including stroke^[13] and overactive bladder.^[14] Although pharmaceutical companies have attempted to develop synthetic molecules targeting BK channels,^[15] their efforts have proved largely ineffective. For instance, BMS-204352 (MaxiPost), a molecule developed by Bristol-Myers Squibb, failed to improve clinical outcome in stroke patients compared to placebo.^[16] BK channels have also been found to be activated by exogenous pollutants and endogenous gazotransmitters carbon monoxide^[17]^[18] and hydrogen sulphide.^[19]

BK channels can be readily inhibited by a range of compounds including tetraethylammonium (TEA), paxilline^[20] and iberiotoxin.^[21]

References

^ Miller C (2000). "An overview of the potassium channel family". Genome Biol. 1 (4): reviews0004.1–reviews0004.5. doi:10.1186/gb-2000-1-4-reviews0004. PMC 138870. PMID 11178249.
^ ^a ^b ^c Yuan P, Leonetti MD, Pico AR, Hsiung Y, MacKinnon R (July 2010). "Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution". Science 329 (5988): 182–6. doi:10.1126/science.1190414. PMC 3022345. PMID 20508092.
^ EntrezGene 3778
^ Davies AG, Pierce-Shimomura JT, Kim H, VanHoven MK, Thiele TR, Bonci A, Bargmann CI, McIntire SL (December 2003). "A central role of the BK potassium channel in behavioral responses to ethanol in C. elegans". Cell 115 (6): 655–66. doi:10.1016/S0092-8674(03)00979-6. PMID 14675531.
^ Alaimo JT, Davis SJ, Song SS, Burnette CR, Grotewiel M, Shelton KL, Pierce-Shimomura JT, Davies AG, Bettinger JC. (April 2012). "Ethanol metabolism and osmolarity modify behavioral responses to ethanol in C. elegans". Alcohol Clin Exp Res 36 (11): 1840–50. doi:10.1111/j.1530-0277.2012.01799.x. PMID 22486589.
^ Wallner M, Meera P, Toro L (December 1996). "Determinant for beta-subunit regulation in high-conductance voltage-activated and Ca(2+)-sensitive K+ channels: an additional transmembrane region at the N terminus". Proc. Natl. Acad. Sci. U.S.A. 93 (25): 14922–7. doi:10.1073/pnas.93.25.14922. PMC 26238. PMID 8962157.
^ ^a ^b ^c Wu Y, Yang Y, Ye S, Jiang Y (July 2010). "Structure of the gating ring from the human large-conductance Ca(2+)-gated K(+) channel". Nature 466 (7304): 393–7. doi:10.1038/nature09252. PMC 2910425. PMID 20574420.
^ Jiang Y, Pico A, Cadene M, Chait BT, MacKinnon R (March 2001). "Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel". Neuron 29 (3): 593–601. doi:10.1016/S0896-6273(01)00236-7. PMID 11301020.
^ Pico AR (2003). RCK domain model of calcium activation in BK channels (PhD thesis). New York: The Rockfeller University. hdl:10209/211.
^ Yusifov T, Savalli N, Gandhi CS, Ottolia M, Olcese R (January 2008). "The RCK2 domain of the human BKCa channel is a calcium sensor". Proc. Natl. Acad. Sci. U.S.A. 105 (1): 376–81. doi:10.1073/pnas.0705261105. PMC 2224220. PMID 18162557.
^ ^a ^b Schreiber M, Salkoff L (September 1997). "A novel calcium-sensing domain in the BK channel". Biophys. J. 73 (3): 1355–63. doi:10.1016/S0006-3495(97)78168-2. PMC 1181035. PMID 9284303.
^ ^a ^b Yuan P, Leonetti MD, Hsiung Y, MacKinnon R (January 2012). "Open structure of the Ca2+ gating ring in the high-conductance Ca2+-activated K+ channel". Nature 481 (7379): 94–7. doi:10.1038/nature10670. PMC 3319005. PMID 22139424.
^ Gribkoff VK, Starrett JE Jr, Dworetzky SI. (2001). "Maxi-K potassium channels: form, function, and modulation of a class of endogenous regulators of intracellular calcium.". Neuroscientist 2: 166–77. doi:10.1177/107385840100700211. PMID 11496927.
^ Jeffrey J. Layne , Bernhard Nausch , Søren-Peter Olesen , Mark T. Nelso (2009). "BK channel activation by NS11021 decreases excitability and contractility of urinary bladder smooth muscle". American Journal of Physiology - Regulatory, Integrative and Comparative Physiology 298 (R378-R384). doi:10.1152/ajpregu.00458.2009. PMID 19923353.
^ Gribkoff VK, Winquist RJ (May 2005). "Voltage-gated cation channel modulators for the treatment of stroke". Expert Opin Investig Drugs 14 (5): 579–92. doi:10.1517/13543784.14.5.579. PMID 15926865.
^ Jensen BS (2002). "BMS-204352: a potassium channel opener developed for the treatment of stroke". CNS Drug Rev 8 (4): 353–60. doi:10.1111/j.1527-3458.2002.tb00233.x. PMID 12481191.
^ Dubuis E, Potier M, Wang R, Vandier C (February 2005). "Continuous inhalation of carbon monoxide attenuates hypoxic pulmonary hypertension development presumably through activation of BKCa channels". Cardiovasc. Res. 65 (3): 751–61. doi:10.1016/j.cardiores.2004.11.007. PMID 15664403.
^ Hou S, Xu R, Heinemann SH, Hoshi T (March 2008). "The RCK1 high-affinity Ca2+ sensor confers carbon monoxide sensitivity to Slo1 BK channels". Proc. Natl. Acad. Sci. U.S.A. 105 (10): 4039–43. doi:10.1073/pnas.0800304105. PMC 2268785. PMID 18316727.
^ Sitdikova GF, Weiger TM, Hermann A (February 2010). "Hydrogen sulfide increases calcium-activated potassium (BK) channel activity of rat pituitary tumor cells". Pflugers Arch. 459 (3): 389–97. doi:10.1007/s00424-009-0737-0. PMID 19802723.
^ "Paxilline, from Fermentek".
^ Candia S, Garcia ML, Latorre R (August 1992). "Mode of action of iberiotoxin, a potent blocker of the large conductance Ca(2+)-activated K+ channel". Biophys. J. 63 (2): 583–90. doi:10.1016/S0006-3495(92)81630-2. PMC 1262182. PMID 1384740.

External links

BK Channels at the US National Library of Medicine Medical Subject Headings (MeSH)
"Calcium-Activated Potassium Channels". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology.

Membrane transport protein: ion channels (TC 1A)

Ca²⁺: Calcium channel

Ligand-gated	Inositol trisphosphate receptor 1 2 3 Ryanodine receptor 1 2 3

Voltage-gated	L-type/Ca_vα 1.1 1.2 1.3 1.4 N-type/Ca_vα2.2 P-type/Ca_vα 2.1 Q-type/Ca_vα2.1 R-type/Ca_vα2.3 T-type/Ca_vα 3.1 3.2 3.3 α₂δ-subunits 1 2 β-subunits β1 β2 β3 β4 γ-subunits γ1 γ2 γ3 γ4 Cation channels of sperm 1 2 3 4 Two-pore channel 1 2

Na⁺: Sodium channel

Constitutively active	Epithelial sodium channel α β γ δ

Proton-gated	Amiloride-sensitive cation channel 1 2 3 4

Voltage-gated	Na_vα 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 7A Na_vβ 1 2 3 4

K⁺: Potassium channel

Calcium-activated	BK channel α1 β1 β2 β3 β4 SK channel SK1 SK2 SK3 IK channel IK1 K_Ca 1.1 2.1 2.2 2.3 3.1 4.1 4.2 5.1

Inward-rectifier	K_ATP K_ir 1.1 2.1 2.2 2.3 2.4 2.6 GIRK/K_ir 3.1 3.2 3.3 3.4 K_ir 4.1 4.2 5.1 6.1 6.2 7.1

Tandem pore domain	K2P 1 2 3 4 5 6 7 9 10 12 13 15 16 17 18

Voltage-gated	K_vα1-6 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 2.1 2.2 3.1 3.2 3.3 3.4 4.1 4.2 4.3 5.1 6.1 6.2 6.3 6.4 K_vα7-12 7.1 7.2 7.3 7.4 7.5 8.1 8.2 9.1 9.2 9.3 10.1 10.2 11.1/hERG 11.2 11.3 12.1 12.2 12.3 K_vβ 1 2 3 KCNIP 1 2 3 4 minK/ISK minK/ISK-like MiRP 1 2 3 Shaker gene

Miscellaneous

Cl^-: Chloride channel	Calcium-activated chloride channels Anoctamin ANO1 Bestrophin 1 2 Chloride Channel Accessory 1 2 3 4 CFTR CLCN 1 2 3 4 5 6 7 KA KB CLIC 1 2 3 4 5 6 L1 CLNS 1A 1B

H⁺: Proton channel	HVCN1

M⁺: CNG cation channel	α 1 2 3 4 β 1 2 3 HCN FC 1 2 3 4

M⁺: TRP cation channel	TRPA (1) TRPC 1 2 3 4 4AP 5 6 7 TRPM 1 2 3 4 5 6 7 8 TRPML 1 2 3 TRPN TRPP 1 2 TRPV 1 2 3 4 5 6

H₂O (+ solutes): Porin	Aquaporin 0 1 2 3 4 5 6 7 8 9 Voltage-dependent anion channel 1 2 3 General bacterial porin family

Cytoplasm: Gap junction	Connexin: A GJA1 GJA3 GJA4 GJA5 GJA8 GJA9 GJA10 B GJB1 GJB2 GJB3 GJB4 GJB5 GJB6 GJB7 C GJC1 GJC2 GJC3 D GJD2 GJD3 GJD4) Innexin

By gating mechanism

Ion channel class	Ligand-gated Light-gated Voltage-gated Stretch-activated

see also disorders
B memb: cead, trns (1A, 1C, 1F, 2A, 3A1, 3A2-3, 3D), other

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Calcium-activated BK potassium channel alpha subunit Provide feedback

No Pfam abstract.

External database links

PANDIT:	PF03493
Pseudofam:	PF03493
SYSTERS:	BK_channel_a

This tab holds annotation information from the InterPro database.

InterPro entry IPR003929

Potassium channels are the most diverse group of the ion channel family [PUBMED:1772658, PUBMED:1879548]. They are important in shaping the action potential, and in neuronal excitability and plasticity [PUBMED:2451788]. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups [PUBMED:2555158]: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group.

These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K⁺ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers [PUBMED:2448635]. In eukaryotic cells, K⁺ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes [PUBMED:1373731]. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis [PUBMED:11178249].

All K⁺ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K⁺ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K⁺ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K⁺ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K⁺ channels; and three types of calcium (Ca)-activated K⁺ channels (BK, IK and SK) [PUBMED:11178249]. The 2TM domain family comprises inward-rectifying K⁺ channels. In addition, there are K⁺ channel alpha-subunits that possess two P-domains. These are usually highly regulated K⁺ selective leak channels.

Ca2+-activated K+ channels are a diverse group of channels that are activated by an increase in intracellular Ca2+ concentration. They are found in the majority of nerve cells, where they modulate cell excitability and action potential. Three types of Ca2+-activated K+ channel have been characterised, termed small-conductance (SK), intermediate conductance (IK) and large conductance (BK) respectively [PUBMED:9687354].

BK channels (also referred to as maxi-K channels) are widely expressed in the body, being found in glandular tissue, smooth and skeletal muscle, as well as in neural tissues. They have been demonstrated to regulate arteriolar and airway diameter, and also neurotransmitter release. Each channel complex is thought to be composed of 2 types of subunit; the pore-forming (alpha) subunits and smaller accessory (beta) subunits.

The alpha subunit of the BK channel was initially thought to share the characteristic 6TM organisation of the voltage-gated K+ channels. However, the molecule is now thought to possess an additional TM domain, with an extracellular N terminus and intracellular C terminus. This C-terminal region contains 4 predominantly hydrophobic domains, which are also thought to lie intracellularly. The extracellular N terminus and the first TM region are required for modulation by the beta subunit. The precise location of the Ca2+-binding site that modulates channel activation remains unknown, but it is thought to lie within the C-terminal hydrophobic domains.

Gene Ontology

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

Cellular component	membrane (GO:0016020)
Molecular function	calcium-activated potassium channel activity (GO:0015269)
Biological process	potassium ion transport (GO:0006813)

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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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 (35)	Full (665)	Representative proteomes				NCBI (608)	Meta (6)
	Seed (35)	Full (665)	RP15 (105)	RP35 (144)	RP55 (218)	RP75 (289)	NCBI (608)	Meta (6)
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HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (35)	Full (665)	Representative proteomes				NCBI (608)	Meta (6)
	Seed (35)	Full (665)	RP15 (105)	RP35 (144)	RP55 (218)	RP75 (289)	NCBI (608)	Meta (6)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (35)	Full (665)	Representative proteomes				NCBI (608)	Meta (6)
	Seed (35)	Full (665)	RP15 (105)	RP35 (144)	RP55 (218)	RP75 (289)	NCBI (608)	Meta (6)
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

Seed source:

PRINTS

Previous IDs:

none

Type:

Family

Author:

Griffiths-Jones SR

Number in seed:

35

Number in full:

665

Average length of the domain:

99.50 aa

Average identity of full alignment:

40 %

Average coverage of the sequence by the domain:

9.24 %

HMM information

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	26.8	26.8
Trusted cut-off	27.5	26.9
Noise cut-off	26.0	26.7

Model length:

101

Family (HMM) version:

13

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

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Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 BK_channel_a domain has been found. There are 10 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 seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: BK_channel_a (PF03493)

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Summary: Calcium-activated BK potassium channel alpha subunit

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Contents

Structure

Pharmacology

See also

References

External links

Calcium-activated BK potassium channel alpha subunit Provide feedback

External database links

InterPro entry IPR003929

Gene Ontology

Domain organisation

Alignments

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How the sunburst is generated

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Unmapped species names

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Species trees

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Structures