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PR01465

Identifier
ELKCHANNEL  [View Relations]  [View Alignment]  
Accession
PR01465
No. of Motifs
6
Creation Date
01-DEC-2000
Title
ELK potassium channel family signature
Database References
PRINTS; PR00169 KCHANNEL; PR01463 EAGCHANLFMLY
Literature References
1. MILLER, C.
An overview of the potassium channel family.
GENOME BIOL. 1(4) 1-5 (2000).
 
2. ASHCROFT, F.M.
Voltage-gated K+ channels.
IN ION CHANNELS AND DISEASE, ACADEMIC PRESS, 2000, PP.97-123.
 
3. LITTLETON, J.T. AND GANETZKY, B.
Ion channels and synaptic organisation: analysis of the Drosophila genome.	
NEURON 26 35-43 (2000).
 
4. MIYAKE, A., MOCHIZUKI, S., YOKOI, H., KOHDA, M. AND FURUICHI, K.
New ether-a-go-go K+ channel family members localised in human
telencephalon.
J.BIOL.CHEM. 274 25018-25025 (1999).  
 
5. TRUDEAU, M.C., TITUS, S.A., BRANCHAW, J.L., GANETZKY, B. 
AND ROBERTSON, G.A.
Functional analysis of a mouse brain Elk-type K+ channel.
J.NEUROSCIENCE 19(8) 2905-2918 (1999).

Documentation
Potassium ion (K+) channels are a structurally diverse group of proteins
that facilitate the flow of K+ ions across cell membranes. They are
ubiquitous, being present in virtually all cell types. Activation of K+
channels tends to hyperpolarise cells, reducing the membrane's electrical
resistance, dampening nervous activity. In eukaryotic cells, K+ channels
are involved in neural signalling and generation of the cardiac rhythm, and
act as effectors in signal transduction pathways involving G protein-
coupled receptors (GPCRs). In prokaryotic cells, they play a role in the
maintenance of ionic homeostasis [1].
 
Structurally, EAG channels belong to the subfamily of K+ channels whose
subunits contain 6 transmembrane (TM) domains: these are the voltage-gated
K+ channels, the KCNQ channels, the EAG-like K+ channels and 3 kinds of
Ca2+-activated K+ channel (BK, IK and SK) [2]. All K+ channels share a
characteristic sequence feature: a TMxTVGYG motif that resides between the
2 C-terminal membrane-spanning helices, and forms the K+-selective pore 
domain [1]. However, unlike other families within this structural class,
EAG channels possess a cyclic nucleotide binding domain within their 
putative intracellular C-termini.
 
The first EAG K+ channel was identified in Drosophila, following a screen 
for mutations giving rise to behavioural abnormalities. Disruption of the
Eag gene caused an ether-induced, leg-shaking behaviour. Subsequent studies
have revealed a conserved multi-gene family of EAG-like K+ channels, which
are present in Homo sapiens and many other species. Based on the varying
functional properties of the channels, the family has been divided into
3 subfamilies: EAG, ELK and ERG. Interestingly, C.elegans appears to lack
the ELK type [3].
 
Little is known about the properties of channels of the ELK subfamily. 
However, when expressed in frog oocytes, they show properties between those
of the EAG and ERG subtypes. Included in this family are Bec1 and Bec2,
brain-specific genes found in the human telencephalon regions. It is thought
that they are involved in cellular excitability of restricted neurons in the
human central nervous system. Phylogenetic analysis reveals that these genes
constitute a subfamily with Elk within the Eag family [4]. Recently, a
further Elk subfamily member has been identified in mouse (Melk). On the
basis of sequence similarity, this indicates a distinct subclass within 
this family [5].
 
ELKCHANNEL is a 6-element fingerprint that provides a signature for the ELK
potassium channel family. The fingerprint was derived from an initial
alignment of 4 sequences: the motifs were drawn from conserved regions 
spanning the full alignment length, focusing on those sections that 
characterise the ELK channels but distinguish them from other members of
the K+ channel superfamily - motifs 1 and 2 reside within the N-terminal
domain; motif 3 spans the loop between putative TM domains 2 and 3; motif 4 
encodes the loop between TM domains 4 and 5; motif 5 spans TM domain 6; and 
motif 6 spans the C-terminal nucleotide binding domain. Three iterations on
SPTR39_14f were required to reach convergence, at which point a true set 
comprising 9 sequences was identified. 
Summary Information
9 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6999999
5000000
4000000
3000000
2000000
123456
True Positives
O88877        O89047        O89048        Q23974        
Q9R1T9 Q9UQ05 Q9UQ06 Q9V899
Q9WVJ0
Sequence Titles
O88877      POTASSIUM CHANNEL - Rattus norvegicus (Rat).  
O89047 ELK CHANNEL 2 (POTASSIUM CHANNEL) - Rattus norvegicus (Rat).
O89048 ELK CHANNEL 1 - Rattus norvegicus (Rat).
Q23974 PUTATIVE POTASSIUM CHANNEL SUBUNIT (EAG-LIKE K[+] CHANNEL PROTEIN) - Drosophila melanogaster (Fruit fly).
Q9R1T9 BEC2 - Rattus norvegicus (Rat).
Q9UQ05 BEC2 - Homo sapiens (Human).
Q9UQ06 BEC1 - Homo sapiens (Human).
Q9V899 ELK PROTEIN - Drosophila melanogaster (Fruit fly).
Q9WVJ0 ETHER-A-GO-GO-LIKE POTASSIUM CHANNEL - Mus musculus (Mouse).
Scan History
SPTR39_14f 3  100  NSINGLE    
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
RKSGLPFWCL O89047 101 101 -
RKDGSAFWCL O89048 101 101 -
KKNGAPFWCL O88877 101 101 -
KKEGAPFWCL Q23974 100 100 -

Motif 2 width=9
Element Seqn Id St Int Rpt
IPIKNEKGE O89047 114 3 -
MPIKNELGE O89048 114 3 -
VPIKNEKGD O88877 114 3 -
VPIKNEKRD Q23974 113 3 -

Motif 3 width=13
Element Seqn Id St Int Rpt
SKSGQVVFAPKSI O89047 286 163 -
SQSGQVVSAPRSI O89048 289 166 -
SKSGQVIFEARSI O88877 282 159 -
SRKGEVVSNSKQI Q23974 323 201 -

Motif 4 width=9
Element Seqn Id St Int Rpt
SQYSAVVLT O89047 353 54 -
SQCSAVVLT O89048 356 54 -
SQHSTIVLT O88877 349 54 -
SQHTAMILT Q23974 392 56 -

Motif 5 width=8
Element Seqn Id St Int Rpt
GALMHAVV O89047 492 130 -
GALMHAVV O89048 464 99 -
GALMHALV O88877 458 100 -
GALMHAVV Q23974 493 92 -

Motif 6 width=11
Element Seqn Id St Int Rpt
EYLIHQGDALQ O89047 610 110 -
EFLLRRGDALQ O89048 582 110 -
EYLLRQGDALQ O88877 576 110 -
EYLIHKGDALN Q23974 611 110 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
RKSGLPFWCL O89047 101 101 -
RKSGLPFWCL Q9UQ06 101 101 -
RKSGLPFWCL Q9WVJ0 101 101 -
RKDGSAFWCL O89048 101 101 -
RKDGSAFWCL Q9R1T9 101 101 -
RKDGSAFWCL Q9UQ05 101 101 -
KKNGAPFWCL O88877 101 101 -
KKEGAPFWCL Q23974 100 100 -
KKEGAPFWCL Q9V899 127 127 -

Motif 2 width=9
Element Seqn Id St Int Rpt
IPIKNEKGE O89047 114 3 -
IPIKNEKGE Q9UQ06 114 3 -
IPIKNEKGE Q9WVJ0 114 3 -
MPIKNELGE O89048 114 3 -
MPIKNELGE Q9R1T9 114 3 -
MPIKNEMGE Q9UQ05 114 3 -
VPIKNEKGD O88877 114 3 -
VPIKNEKRD Q23974 113 3 -
VPIKNEKRD Q9V899 140 3 -

Motif 3 width=13
Element Seqn Id St Int Rpt
SKSGQVVFAPKSI O89047 286 163 -
SKSGQVVFAPKSI Q9UQ06 286 163 -
SKSGQVVFAPKSI Q9WVJ0 286 163 -
SQSGQVVSAPRSI O89048 289 166 -
SQSGQVVSAPRSI Q9R1T9 289 166 -
SQSGQVISAPRSI Q9UQ05 288 165 -
SKSGQVIFEARSI O88877 282 159 -
SRKGEVVSNSKQI Q23974 323 201 -
SRKGEVVSNSKQI Q9V899 350 201 -

Motif 4 width=9
Element Seqn Id St Int Rpt
SQYSAVVLT O89047 353 54 -
SQYSAVVLT Q9UQ06 353 54 -
SQYSAVVLT Q9WVJ0 353 54 -
SQCSAVVLT O89048 356 54 -
SQCSAVVLT Q9R1T9 356 54 -
SQCSAVVLT Q9UQ05 355 54 -
SQHSTIVLT O88877 349 54 -
SQHTAMILT Q23974 392 56 -
SQHTAMILT Q9V899 419 56 -

Motif 5 width=8
Element Seqn Id St Int Rpt
GALMHAVV O89047 492 130 -
GALMHAVV Q9UQ06 489 127 -
GALMHAVV Q9WVJ0 492 130 -
GALMHAVV O89048 464 99 -
GALMHAVV Q9R1T9 464 99 -
GALMHAVV Q9UQ05 463 99 -
GALMHALV O88877 458 100 -
GALMHAVV Q23974 493 92 -
GALMHAVV Q9V899 520 92 -

Motif 6 width=11
Element Seqn Id St Int Rpt
EYLIHQGDALQ O89047 610 110 -
EYLIHQGDALQ Q9UQ06 607 110 -
EYLIHQGDALQ Q9WVJ0 610 110 -
EFLLRRGDALQ O89048 582 110 -
EFLLRRGDALQ Q9R1T9 582 110 -
EYLLRRGDALQ Q9UQ05 581 110 -
EYLLRQGDALQ O88877 576 110 -
EYLIHKGDALN Q23974 611 110 -
EYLIHKGDALN Q9V899 638 110 -