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PR01513

Identifier
KV16CHANNEL  [View Relations]  [View Alignment]  
Accession
PR01513
No. of Motifs
10
Creation Date
21-JUN-2001
Title
Kv1.6 voltage-gated K+ channel signature
Database References
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. SANSOM, M.S.
Putting the parts together.
CURR.BIOL. 9(19) R738-R741 (1999).   
 
4. LITTLETON, J.T. AND GANETZKY, B.
Ion Channels and synaptic organisation: analysis of the Drosophila genome.   
NEURON 26 35-43 (2000).
 
5. CONLEY, E.C. AND BRAMMAR, W.J.
Shaker.
IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.559-614.

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, Kv channels belong to the subfamily of K+ channels whose
subunits contain 6 transmembrane (TM) domains: these are the voltage-
gated K+ (Kv) channels, the KCNQ channels, the EAG-like K+ channels and
3 kinds of Ca2+-activated K+ channels (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 [1-2].
     
The Kv family can be divided into 4 subfamilies on the basis of sequence
similarity and function: Shaker (Kv1), Shab (Kv2), Shaw (Kv3) and Shal 
(Kv4). All consist of pore-forming alpha subunits that associate with 
different types of beta subunit. To form a functional K+ channel pore,
4 alpha subunits and 4 beta subunits are required. The alpha subunits
have 6 well-conserved TM domains, a pore loop region and variable length
N- and C-termini. TM domains 5 and 6, and the loop region, form the K+ 
channel pore through which the K+ ions pass [3].
     
The first Shaker (Kv1) sequence was found in Drosophila. Several vertebrate
K+ channels with similar amino acid sequences were subsequently found and,
together with the Drosophila Shaker channel, now constitute the Shaker (Kv1) 
family. These channels are mostly expressed in the brain, but can also be
found in non-excitable cells, such as lymphocytes [4,5].  
 
Kv1.6 is expressed in the heart, smooth muscle cells and brain, especially
the midbrain areas and brainstem. The kv1.6 alpha-subunits can also
coassemble with other Shaker alpha subunits, for example, with kv1.5 to
form heteromultimeric K+ channels [5].
 
KV16CHANNEL is a 10-element fingerprint that provides a signature for the
Kv1.6 voltage-gated potassium channel. The fingerprint was derived from an
initial alignment of 3 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length - motifs 1-5 reside at
the N-terminus; motifs 6-8 lie between the first and second putative TM 
domains; and motifs 9 and 10 reside at the C-terminus. A single iteration
on SPTR39_15f was required to reach convergence, no further sequences being 
identified beyond the starting set. Two partial matches were found,
both of which are members of the Shaker family that match 2 motifs.
Summary Information
   3 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
103333333333
90000000000
80000000000
70000000000
60000000000
50000000000
40000000000
30000000000
20012000010
12345678910
True Positives
CIK6_HUMAN    CIK6_RAT      Q61923        
True Positive Partials
Codes involving 2 elements
CIK3_MOUSE Q9I829
Sequence Titles
CIK6_HUMAN  VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV1.6 (HBK2) - Homo sapiens (Human). 
CIK6_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV1.6 (RCK2) (KV2) - Rattus norvegicus (Rat).
Q61923 MURINE POTASSIUM CHANNEL PROTEIN - Mus musculus (Mouse).

CIK3_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV1.3 (MK3) - Mus musculus (Mouse).
Q9I829 SHAKER-RELATED POTASSIUM CHANNEL TSHA2 - Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri).
Scan History
SPTR39_15f 1  50   NSINGLE    
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
MRSEKSLTLAAPGE Q61923 1 1 -
MRSEKSLTLAAPGE CIK6_RAT 1 1 -
MRSEKSLTLAAPGE CIK6_HUMAN 1 1 -

Motif 2 width=14
Element Seqn Id St Int Rpt
RGPEGEQQDAGEFQ Q61923 16 1 -
RGPEGEQQDAGEFQ CIK6_RAT 16 1 -
RGPEGEQQDAGDFP CIK6_HUMAN 16 1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EGGGGCCSSERLV Q61923 32 2 -
EGGGGCCSSERLV CIK6_RAT 32 2 -
GGGGGCCSSERLV CIK6_HUMAN 32 2 -

Motif 4 width=12
Element Seqn Id St Int Rpt
QLRTLSLFPDTL Q61923 55 10 -
QLRTLSLFPDTL CIK6_RAT 55 10 -
QLRTLSLFPDTL CIK6_HUMAN 55 10 -

Motif 5 width=13
Element Seqn Id St Int Rpt
EDEGCLPEGGEDE Q61923 136 69 -
EDEGCLPEGGEDE CIK6_RAT 136 69 -
EDEGCLPEGGEDE CIK6_HUMAN 136 69 -

Motif 6 width=14
Element Seqn Id St Int Rpt
SHEEEDEDEDSYAF Q61923 221 72 -
SHEEEDEDEDSYAF CIK6_RAT 222 73 -
SQEEEEDEDDSYTF CIK6_HUMAN 221 72 -

Motif 7 width=12
Element Seqn Id St Int Rpt
GSIPSGGLGTGG Q61923 236 1 -
GSIPSGGLGTGG CIK6_RAT 237 1 -
HGITPGEMGTGG CIK6_HUMAN 236 1 -

Motif 8 width=12
Element Seqn Id St Int Rpt
SSLSTLGGSFFT Q61923 249 1 -
SSFSTLGGSFFT CIK6_RAT 250 1 -
SSLSTLGGSFFT CIK6_HUMAN 249 1 -

Motif 9 width=15
Element Seqn Id St Int Rpt
QGQYTHVTCGQPTPD Q61923 474 213 -
QGQYTHVTCGQPTPD CIK6_RAT 475 213 -
QGQYTHVTCGQPAPD CIK6_HUMAN 474 213 -

Motif 10 width=16
Element Seqn Id St Int Rpt
FAEASRERRPSYLPTP Q61923 501 12 -
FAEASRERRSSYLPTP CIK6_RAT 502 12 -
FPEANRERRPSYLPTP CIK6_HUMAN 501 12 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
MRSEKSLTLAAPGE Q61923 1 1 -
MRSEKSLTLAAPGE CIK6_RAT 1 1 -
MRSEKSLTLAAPGE CIK6_HUMAN 1 1 -

Motif 2 width=14
Element Seqn Id St Int Rpt
RGPEGEQQDAGEFQ Q61923 16 1 -
RGPEGEQQDAGEFQ CIK6_RAT 16 1 -
RGPEGEQQDAGDFP CIK6_HUMAN 16 1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EGGGGCCSSERLV Q61923 32 2 -
EGGGGCCSSERLV CIK6_RAT 32 2 -
GGGGGCCSSERLV CIK6_HUMAN 32 2 -

Motif 4 width=12
Element Seqn Id St Int Rpt
QLRTLSLFPDTL Q61923 55 10 -
QLRTLSLFPDTL CIK6_RAT 55 10 -
QLRTLSLFPDTL CIK6_HUMAN 55 10 -

Motif 5 width=13
Element Seqn Id St Int Rpt
EDEGCLPEGGEDE Q61923 136 69 -
EDEGCLPEGGEDE CIK6_RAT 136 69 -
EDEGCLPEGGEDE CIK6_HUMAN 136 69 -

Motif 6 width=14
Element Seqn Id St Int Rpt
SHEEEDEDEDSYAF Q61923 221 72 -
SHEEEDEDEDSYAF CIK6_RAT 222 73 -
SQEEEEDEDDSYTF CIK6_HUMAN 221 72 -

Motif 7 width=12
Element Seqn Id St Int Rpt
GSIPSGGLGTGG Q61923 236 1 -
GSIPSGGLGTGG CIK6_RAT 237 1 -
HGITPGEMGTGG CIK6_HUMAN 236 1 -

Motif 8 width=12
Element Seqn Id St Int Rpt
SSLSTLGGSFFT Q61923 249 1 -
SSFSTLGGSFFT CIK6_RAT 250 1 -
SSLSTLGGSFFT CIK6_HUMAN 249 1 -

Motif 9 width=15
Element Seqn Id St Int Rpt
QGQYTHVTCGQPTPD Q61923 474 213 -
QGQYTHVTCGQPTPD CIK6_RAT 475 213 -
QGQYTHVTCGQPAPD CIK6_HUMAN 474 213 -

Motif 10 width=16
Element Seqn Id St Int Rpt
FAEASRERRPSYLPTP Q61923 501 12 -
FAEASRERRSSYLPTP CIK6_RAT 502 12 -
FPEANRERRPSYLPTP CIK6_HUMAN 501 12 -