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331  structures 1797  species 1  interaction 10724  sequences 199  architectures

Family: Ion_trans_2 (PF07885)

Summary: Ion channel

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Ion channel family". More...

Ion channel family Edit Wikipedia article

Ion channel (eukaryotic)
2r9r opm.png
Potassium channel Kv1.2 (with beta2 auxiliary subunits), structure in a membrane-like environment. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Identifiers
Symbol Ion_trans
Pfam PF00520
InterPro IPR005821
SCOP 1bl8
SUPERFAMILY 1bl8
TCDB 1.A.1
OPM superfamily 8
OPM protein 2a79
Ion channel (bacterial)
1r3j.png
Potassium channel KcsA. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Identifiers
Symbol Ion_trans_2
Pfam PF07885
InterPro IPR013099
SCOP 1bl8
SUPERFAMILY 1bl8
OPM protein 1r3j

Transmembrane cation channel superfamily was defined in InterPro and Pfam as the family of tetrameric ion channels. These include the sodium, potassium,[1] calcium, ryanodine receptor, HCN, CNG, CatSper, and TRP channels. This large group of ion channels apparently includes families 1.A.1, 1.A.2, 1.A.3, and 1.A.4 of the TCDB transporter classification.

They are described as minimally having two transmembrane helices flanking a loop which determines the ion selectivity of the channel pore. Many eukaryotic channels have four additional transmembrane helices (TM) (Pfam PF00520), related to or vestigial of voltage gating. The proteins with only two transmembrane helices (Pfam PF07885) are most commonly found in bacteria. This also includes the 2-TM Inward-rectifier potassium channels (Pfam PF01007) found primarily in eukaryotes. There are commonly additional regulatory domains which serve to regulate ion conduction and channel gating. The pores may also be homotetramers or hetrotetramers; where hetrotetramers may be encoded as distinct genes or as multiple pore domains within a single polypepetide. Interestingly, the HVCN1 and Putative tyrosine-protein phosphatase proteins do not contain an expected ion conduction pore domain, but rather have homology only to the voltage sensor domain of voltage gated ion channels.

Human channels with 6 TM helices

Cation

Transient receptor potential channel

Canonical TRP Channels
Melastatin TRP Channels
Vanilloid TRP Channels
Mucolipin TRP Channels
Ankyrin TRP Channels
TRPP

Calcium

Voltage-dependent calcium channel

Cation channels of sperm

Ryanodine receptor

Potassium

Voltage-gated potassium channels

Delayed rectifier
A-type potassium channel
  • Kvα1.x - Shaker-related: Kv1.4 (KCNA4)
  • Kvα3.x - Shaw-related: Kv3.3 (KCNC3), Kv3.4 (KCNC4)
  • Kvα4.x - Shal-related: Kv4.1 (KCND1), Kv4.2 (KCND2), Kv4.3 (KCND3)
Outward-rectifying
  • Kvα10.x: Kv10.2 (KCNH5)
Inwardly-rectifying
Slowly activating
Modifier/silencer

Calcium-activated potassium channel

BK channel
SK channel
  • KCa2.x: KCa2.1 (KCNN1) - SK1, KCa2.2 (KCNN2) - SK2, KCa2.3 (KCNN3) - SK3
  • KCa3.x: KCa3.1 (KCNN4) - SK4
  • KCa4.x: KCa4.1 (KCNT1) - SLACK, KCa4.2 (KCNT2) - SLICK
IK channel
Other subfamilies

Inward-rectifier potassium ion channel

Sodium

Cyclic nucleotide-gated

Proton

Related Proteins

Human channels with 2 TM helices in each subunit

Potassium

Tandem pore domain potassium channel

Non-human Channels

Two-pore channels

Pore-only Potassium Channels

Ligand Gated Potassium Channel

Voltage-gated Potassium Channels

Prokaryotic KCa Channels

Voltage and Cyclic Nucleotide Gated Potassium Channel

Sodium Channels

Non-Selective Channels

Prokaryotic Inward-rectifier potassium channels

Engineered Channels

References

  1. ^ Choe S (February 2002). "Potassium channel structures". Nat. Rev. Neurosci. 3 (2): 115–21. doi:10.1038/nrn727. PMID 11836519. 
  2. ^ Chen, GQ; Cui, C; Mayer, ML; Gouaux, E (16 December 1999). "Functional characterization of a potassium-selective prokaryotic glutamate receptor.". Nature 402 (6763): 817–21. PMID 10617203. 
  3. ^ Jiang, Y; Lee, A; Chen, J; Ruta, V; Cadene, M; Chait, BT; MacKinnon, R (1 May 2003). "X-ray structure of a voltage-dependent K+ channel.". Nature 423 (6935): 33–41. PMID 12721618. 
  4. ^ Milkman R (Apr 1994). "An Escherichia coli homologue of eukaryotic potassium channel proteins". Proceedings of the National Academy of Sciences of the United States of America 91 (9): 3510–4. PMID 8170937. 
  5. ^ Jiang Y, Pico A, Cadene M, Chait BT, MacKinnon R (Mar 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. PMID 11301020. 
  6. ^ Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R (May 2002). "Crystal structure and mechanism of a calcium-gated potassium channel". Nature 417 (6888): 515–22. Bibcode:2002Natur.417..515J. doi:10.1038/417515a. PMID 12037559. 
  7. ^ Smith FJ, Pau VP, Cingolani G, Rothberg BS (2013). "Structural basis of allosteric interactions among Ca2+-binding sites in a K+ channel RCK domain". Nature Communications 4: 2621. Bibcode:2013NatCo...4E2621S. doi:10.1038/ncomms3621. PMID 24126388. 
  8. ^ Ye S, Li Y, Chen L, Jiang Y (Sep 2006). "Crystal structures of a ligand-free MthK gating ring: insights into the ligand gating mechanism of K+ channels". Cell 126 (6): 1161–73. doi:10.1016/j.cell.2006.08.029. PMID 16990139. 
  9. ^ Dvir H, Valera E, Choe S (Aug 2010). "Structure of the MthK RCK in complex with cadmium". Journal of Structural Biology 171 (2): 231–7. doi:10.1016/j.jsb.2010.03.020. PMID 20371380. 
  10. ^ Smith FJ, Pau VP, Cingolani G, Rothberg BS (Dec 2012). "Crystal structure of a Ba(2+)-bound gating ring reveals elementary steps in RCK domain activation". Structure 20 (12): 2038–47. doi:10.1016/j.str.2012.09.014. PMID 23085076. 
  11. ^ Cao Y, Jin X, Huang H, Derebe MG, Levin EJ, Kabaleeswaran V, et al. (Mar 2011). "Crystal structure of a potassium ion transporter, TrkH". Nature 471 (7338): 336–40. Bibcode:2011Natur.471..336C. doi:10.1038/nature09731. PMC 3077569. PMID 21317882. 
  12. ^ Cao Y, Pan Y, Huang H, Jin X, Levin EJ, Kloss B, et al. (Apr 2013). "Gating of the TrkH ion channel by its associated RCK protein TrkA". Nature 496 (7445): 317–22. Bibcode:2013Natur.496..317C. doi:10.1038/nature12056. PMC 3726529. PMID 23598339. 
  13. ^ Vieira-Pires RS, Szollosi A, Morais-Cabral JH (Apr 2013). "The structure of the KtrAB potassium transporter". Nature 496 (7445): 323–8. Bibcode:2013Natur.496..323V. doi:10.1038/nature12055. PMID 23598340. 
  14. ^ Kong C, Zeng W, Ye S, Chen L, Sauer DB, Lam Y, et al. (2012). "Distinct gating mechanisms revealed by the structures of a multi-ligand gated K(+) channel". eLife 1: e00184. doi:10.7554/eLife.00184. PMC 3510474. PMID 23240087. 
  15. ^ Deller MC, Johnson HA, Miller MD, Spraggon G, Elsliger MA, Wilson IA, et al. (2015). "Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly". PloS One 10 (3): e0122512. doi:10.1371/journal.pone.0122512. PMC 4380455. PMID 25826626. 
  16. ^ Clayton, GM; Altieri, S; Heginbotham, L; Unger, VM; Morais-Cabral, JH (5 February 2008). "Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel.". Proceedings of the National Academy of Sciences of the United States of America 105 (5): 1511–5. PMID 18216238. 
  17. ^ Ren, D; Navarro, B; Xu, H; Yue, L; Shi, Q; Clapham, DE (14 December 2001). "A prokaryotic voltage-gated sodium channel.". Science (New York, N.Y.) 294 (5550): 2372–5. PMID 11743207. 
  18. ^ Payandeh, J; Scheuer, T; Zheng, N; Catterall, WA (10 July 2011). "The crystal structure of a voltage-gated sodium channel.". Nature 475 (7356): 353–8. PMID 21743477. 
  19. ^ Shaya, D; Findeisen, F; Abderemane-Ali, F; Arrigoni, C; Wong, S; Nurva, SR; Loussouarn, G; Minor DL, Jr (23 January 2014). "Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.". Journal of molecular biology 426 (2): 467–83. PMID 24120938. 
  20. ^ Zhang, X; Ren, W; DeCaen, P; Yan, C; Tao, X; Tang, L; Wang, J; Hasegawa, K; Kumasaka, T; He, J; Wang, J; Clapham, DE; Yan, N (20 May 2012). "Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel.". Nature 486 (7401): 130–4. PMID 22678295. 
  21. ^ McCusker, EC; Bagnéris, C; Naylor, CE; Cole, AR; D'Avanzo, N; Nichols, CG; Wallace, BA (2012). "Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.". Nature communications 3: 1102. PMID 23033078. 
  22. ^ Shi, N; Ye, S; Alam, A; Chen, L; Jiang, Y (23 March 2006). "Atomic structure of a Na+- and K+-conducting channel.". Nature 440 (7083): 570–4. PMID 16467789. 
  23. ^ Durell, SR; Guy, HR (2001). "A family of putative Kir potassium channels in prokaryotes.". BMC evolutionary biology 1: 14. PMID 11806753. 
  24. ^ Derebe, MG; Sauer, DB; Zeng, W; Alam, A; Shi, N; Jiang, Y (11 January 2011). "Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites.". Proceedings of the National Academy of Sciences of the United States of America 108 (2): 598–602. PMID 21187421. 
  25. ^ Sauer, DB; Zeng, W; Raghunathan, S; Jiang, Y (4 October 2011). "Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation.". Proceedings of the National Academy of Sciences of the United States of America 108 (40): 16634–9. PMID 21933962. 

External links

This article incorporates text from the public domain Pfam and InterPro IPR005821

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

This is the Wikipedia entry entitled "Voltage-gated potassium channel". More...

Voltage-gated potassium channel Edit Wikipedia article

Ion channel (eukaryotic)
2r9r opm.png
Potassium channel, structure in a membrane-like environment. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Identifiers
Symbol Ion_trans
Pfam PF00520
InterPro IPR005821
SCOP 1bl8
SUPERFAMILY 1bl8
TCDB 1.A.1
OPM superfamily 8
OPM protein 2a79
Ion channel (bacterial)
1r3j.png
Potassium channel KcsA. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Identifiers
Symbol Ion_trans_2
Pfam PF07885
InterPro IPR013099
SCOP 1bl8
SUPERFAMILY 1bl8
OPM protein 1r3j
Slow voltage-gated potassium channel (Potassium channel, voltage-dependent, beta subunit, KCNE)
Identifiers
Symbol ISK_Channel
Pfam PF02060
InterPro IPR000369
TCDB 8.A.10
KCNQ voltage-gated potassium channe
Identifiers
Symbol KCNQ_channel
Pfam PF03520
InterPro IPR013821
Kv2 voltage-gated K+ channel
Identifiers
Symbol Kv2channel
Pfam PF03521
InterPro IPR003973

Voltage-gated potassium channels (VGKCs) are transmembrane channels specific for potassium and sensitive to voltage changes in the cell's membrane potential. During action potentials, they play a crucial role in returning the depolarized cell to a resting state.

Classification

Alpha subunits

Alpha subunits form the actual conductance pore. Based on sequence homology of the hydrophobic transmembrane cores, the alpha subunits of voltage-gated potassium channels are grouped into 12 classes. These are labeled Kvα1-12.[1] The following is a list of the 40 known human voltage-gated potassium channel alpha subunits grouped first according to function and then subgrouped according to the Kv sequence homology classification scheme:

Delayed rectifier

slowly inactivating or non-inactivating

A-type potassium channel

rapidly inactivating

  • Kvα1.x - Shaker-related: Kv1.4 (KCNA4)
  • Kvα3.x - Shaw-related: Kv3.3 (KCNC3), Kv3.4 (KCNC4)
  • Kvα4.x - Shal-related: Kv4.1 (KCND1), Kv4.2 (KCND2), Kv4.3 (KCND3)

Outward-rectifying

  • Kvα10.x: Kv10.2 (KCNH5)

Inwardly-rectifying

Passes current more easily in the inward direction (into the cell, from outside).

Slowly activating

Modifier/silencer

Unable to form functional channels as homotetramers but instead heterotetramerize with Kvα2 family members to form conductive channels.

Beta subunits

Beta subunits are auxiliary proteins that associate with alpha subunits, sometimes in a α4β4 stoichiometry.[2] These subunits do not conduct current on their own but rather modulate the activity of Kv channels.[3]

Proteins minK and MiRP1 are putative hERG beta subunits.[6]

Animal research

The voltage-gated K+ channels that provide the outward currents of action potentials have similarities to bacterial K+ channels.

These channels have been studied by X-ray diffraction, allowing determination of structural features at atomic resolution.

The function of these channels is explored by electrophysiological studies.

Genetic approaches include screening for behavioral changes in animals with mutations in K+ channel genes. Such genetic methods allowed the genetic identification of the "Shaker" K+ channel gene in Drosophila before ion channel gene sequences were well known.

Study of the altered properties of voltage-gated K+ channel proteins produced by mutated genes has helped reveal the functional roles of K+ channel protein domains and even individual amino acids within their structures.

Structure

Typically, vertebrate voltage-gated K+ channels are tetramers of four identical subunits arranged as a ring, each contributing to the wall of the trans-membrane K+ pore. Each subunit is composed of six membrane spanning hydrophobic α-helical sequences. The high resolution crystallographic structure of the rat Kvα1.2/β2 channel has recently been solved (Protein Databank Accession Number 2A79​),[7] and then refined in a lipid membrane-like environment (PDB: 2r9r​).

Selectivity

Voltage-gated K+ channels are selective for K+ over other cations such as Na+. There is a selectivity filter at the narrowest part of the transmembrane pore.

Channel mutation studies have revealed the parts of the subunits that are essential for ion selectivity. They include the amino acid sequence (Thr-Val-Gly-Tyr-Gly) or (Thr-Val-Gly-Phe-Gly) typical to the selectivity filter of voltage-gated K+ channels. As K+ passes through the pore, interactions between potassium ions and water molecules are prevented and the K+ interacts with specific atomic components of the Thr-Val-Gly-[YF]-Gly sequences from the four channel subunits [1].

It may seem counterintuitive that a channel should allow potassium ions but not the smaller sodium ions through. However in an aqueous environment, potassium and sodium cations are solvated by water molecules. When moving through the selectivity filter of the potassium channel, the water-K+ interactions are replaced by interactions between K+ and carbonyl groups of the channel protein. The diameter of the selectivity filter is ideal for the potassium cation, but too big for the smaller sodium cation. Hence the potassium cations are well "solvated" by the protein carbonyl groups, but these same carbonyl groups are too far apart to adequately solvate the sodium cation. Hence, the passage of potassium cations through this selectivity filter is strongly favored over sodium cations.

Open and closed conformations

The structure of the mammalian voltage-gated K+ channel has been used to explain its ability to respond to the voltage across the membrane. Upon opening of the channel, conformational changes in the voltage-sensor domains (VSD) result in the transfer of 12-13 elementary charges across the membrane electric field. This charge transfer is measured as a transient capacitive current that precedes opening of the channel. Several charged residues of the VSD, in particular four arginine residues located regularly at every third position on the S4 segment, are known to move across the transmembrane field and contribute to the gating charge. The position of these arginines, known as gating arginines, are highly conserved in all voltage-gated potassium, sodium, or calcium channels. However, the extent of their movement and their displacement across the transmembrane potential has been subject to extensive debate.[8] Specific domains of the channel subunits have been identified that are responsible for voltage-sensing and converting between the open and closed conformations of the channel. There are at least two closed conformations. In the first, the channel can open if the membrane potential becomes more positive. This type of gating is mediated by a voltage-sensing domain that consists of the S4 alpha helix that contains 6–7 positive charges. Changes in membrane potential cause this alpha helix to move in the lipid bilayer. This movement in turn results in a conformational change in the adjacent S5–S6 helices that form the channel pore and cause this pore to open or close. In the second, "N-type" inactivation, voltage-gated K+ channels inactivate after opening, entering a distinctive, closed conformation. In this inactivated conformation, the channel cannot open, even if the transmembrane voltage is favorable. The amino terminal domain of the K+ channel or an auxiliary protein can mediate "N-type" inactivation. The mechanism of this type of inactivation has been described as a "ball and chain" model, where the N-terminus of the protein forms a ball that is tethered to the rest of the protein through a loop (the chain).[9] The tethered ball blocks the inner porehole, preventing ion movement through the channel.[10][11]

See also

References

  1. ^ Gutman GA, Chandy KG, Grissmer S, Lazdunski M, McKinnon D, Pardo LA, Robertson GA, Rudy B, Sanguinetti MC, Stuhmer W, Wang X (2005). "International Union of Pharmacology. LIII. Nomenclature and molecular relationships of voltage-gated potassium channels.". Pharmacol Rev 57 (4): 473–508. doi:10.1124/pr.57.4.10. PMID 16382104. 
  2. ^ Pongs O, Leicher T, Berger M, Roeper J, Bahring R, Wray D, Giese KP, Silva AJ, Storm JF (1999). "Functional and molecular aspects of voltage-gated K+ channel beta subunits". Ann N Y Acad Sci 868 (Apr 30): 344–55. doi:10.1111/j.1749-6632.1999.tb11296.x. PMID 10414304. 
  3. ^ Li Y, Um SY, McDonald TV (2006). "Voltage-gated potassium channels: regulation by accessory subunits". Neuroscientist 12 (3): 199–210. doi:10.1177/1073858406287717. PMID 16684966. 
  4. ^ Zhang M, Jiang M, Tseng GN (2001). "minK-related peptide 1 associates with Kv4.2 and modulates its gating function: potential role as beta subunit of cardiac transient outward channel?". Circ Res 88 (10): 1012–9. doi:10.1161/hh1001.090839. PMID 11375270. 
  5. ^ McCrossan ZA, Abbott GW (2004). "The MinK-related peptides". Neuropharmacology 47 (6): 787–821. doi:10.1016/j.neuropharm.2004.06.018. PMID 15527815. 
  6. ^ Anantharam A, Abbott GW (2005). "Does hERG coassemble with a beta subunit? Evidence for roles of MinK and MiRP1". Novartis Found Symp 266 (42): 112–7, 155–8. doi:10.1002/047002142X.fmatter. PMID 16050264. 
  7. ^ Long SB, Campbell EB, Mackinnon R (2005). "Crystal structure of a mammalian voltage-dependent Shaker family K+ channel". Science 309 (5736): 897–903. doi:10.1126/science.1116269. PMID 16002581. 
  8. ^ Lee S, Lee A, Chen J, MacKinnon R (2005). "Structure of the KvAP voltage-dependent K+ channel and its dependence on the lipid membrane.". Proc Natl Acad Sci USA 102 (43): 15441–6. doi:10.1073/pnas.0507651102. PMC 1253646. PMID 16223877. 
  9. ^ Antz C, Fakler B (August 1998). "Fast Inactivation of Voltage-Gated K(+) Channels: From Cartoon to Structure" (PDF). News Physiol. Sci. 13 (4): 177–182. PMID 11390785. 
  10. ^ Armstrong CM, Bezanilla F (April 1973). "Currents related to movement of the gating particles of the sodium channels". Nature 242 (5398): 459–61. doi:10.1038/242459a0. PMID 4700900. 
  11. ^ Murrell-Lagnado RD, Aldrich RW (December 1993). "Energetics of Shaker K channels block by inactivation peptides". J. Gen. Physiol. 102 (6): 977–1003. doi:10.1085/jgp.102.6.977. PMC 2229186. PMID 8133246. 

External links

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.

Ion channel Provide feedback

This family includes the two membrane helix type ion channels found in bacteria.

Literature references

  1. Choe S; , Nat Rev Neurosci 2002;3:115-121.: Potassium channel structures. PUBMED:11836519 EPMC:11836519


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013099

This domain is found in a variety of potassium channel proteins, including the two membrane helix type ion channels found in bacteria [PUBMED:11836519].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Ion_channel (CL0030), which has the following description:

This superfamily contains a diverse range of ion channels that share a pair of transmembrane helices in common. This clan is classified as the VIC (Voltage-gated Ion Channel) superfamily in TCDB.

The clan contains the following 7 members:

Ion_trans Ion_trans_2 IRK KdpA Lig_chan PKD_channel TrkH

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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  Seed
(104)
Full
(10724)
Representative proteomes UniProt
(23617)
NCBI
(60889)
Meta
(1621)
RP15
(3394)
RP35
(6349)
RP55
(9996)
RP75
(13253)
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  Seed
(104)
Full
(10724)
Representative proteomes UniProt
(23617)
NCBI
(60889)
Meta
(1621)
RP15
(3394)
RP35
(6349)
RP55
(9996)
RP75
(13253)
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  Seed
(104)
Full
(10724)
Representative proteomes UniProt
(23617)
NCBI
(60889)
Meta
(1621)
RP15
(3394)
RP35
(6349)
RP55
(9996)
RP75
(13253)
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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.

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_55 (release 15.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 104
Number in full: 10724
Average length of the domain: 80.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 22.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.5 22.5
Trusted cut-off 22.5 22.5
Noise cut-off 22.4 22.4
Model length: 79
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There is 1 interaction for this family. More...

Ion_trans_2

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 Ion_trans_2 domain has been found. There are 331 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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