SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR01498

Identifier
SHAWCHANNEL  [View Relations]  [View Alignment]  
Accession
PR01498
No. of Motifs
5
Creation Date
26-FEB-2001
Title
Shaw voltage-gated K+ channel family signature
Database References
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01581 KV31CHANNEL
PRINTS; PR01582 KV33CHANNEL; PR01583 KV34CHANNEL
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. CONLEY, E.C. AND BRAMMAR, W.J.
Shaw.
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 5/6 and the loop region form the K+ 
channel pore through which the K+ ions pass [3]. 
 
The shaw gene was first isolated from Drosophila. Several vertebrate K+
channels with similar amino acid sequences were subsequently found and,
together with the Drosophila Shaw channel, now constitute the Shaw (Kv3)
family. These channels are thought to play a role in shortening of action
potential durations and modulating pre-synaptic neurotransmitter release.
In mammals, the family consists of 4 genes (Kv3.1, Kv3.2, Kv3.3 and Kv3.4).
Each gene product has its own subcellular location and function [4].
 
SHAWCHANNEL is a 5-element fingerprint that provides a signature for the
Shaw voltage-gated K+ channel family. The fingerprint was derived from an
initial alignment of 6 sequences: the motifs were drawn from conserved
regions spanning the full alignment lenth: motifs 1 and 2 reside within the
N-terminus; motif 3 spans the N-terminus and part of TM domain 1; motif 4
spans the loop between TM domains 2 and 3; and motif 5 resides in the
C-terminal domain. Three iterations on SPTR39_14f were required to reach
convergence, at which point a true set comprising 18 sequences was 
identified. 
Summary Information
18 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
51818181818
400000
300000
200000
12345
True Positives
CIKD_HUMAN    CIKD_MOUSE    CIKD_RAT      CIKE_RAT      
CIKF_HUMAN CIKF_MOUSE CIKF_RAT CIKG_HUMAN
CIKG_RAT CIKW_DROME O62350 O76457
Q19464 Q22012 Q26041 Q9PVD1
Q9VLC6 Q9XSJ8
Sequence Titles
CIKD_HUMAN  VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) - Homo sapiens (Human). 
CIKD_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) - Mus musculus (Mouse).
CIKD_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) (RAW2) - Rattus norvegicus (Rat).
CIKE_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.2 (KSHIIIA) - Rattus norvegicus (Rat).
CIKF_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Homo sapiens (Human).
CIKF_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Mus musculus (Mouse).
CIKF_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Rattus norvegicus (Rat).
CIKG_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (KSHIIIC) - Homo sapiens (Human).
CIKG_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (RAW3) - Rattus norvegicus (Rat).
CIKW_DROME VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN SHAW (SHAW2) - Drosophila melanogaster (Fruit fly).
O62350 EGL-36 PROTEIN - Caenorhabditis elegans.
O76457 SHAW POTASSIUM CHANNEL KV3.1A - Aplysia californica (California sea hare).
Q19464 F14F11.1 PROTEIN - Caenorhabditis elegans.
Q22012 R186.5 PROTEIN - Caenorhabditis elegans.
Q26041 SHAW POTASSIUM CHANNEL - Panulirus interruptus (California spiny lobster).
Q9PVD1 KV3.1 POTASSIUM CHANNEL - Xenopus laevis (African clawed frog).
Q9VLC6 CG4450 PROTEIN - Drosophila melanogaster (Fruit fly).
Q9XSJ8 KV3.1 - Canis familiaris (Dog).
Scan History
SPTR39_14f 3  20   NSINGLE    
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
FFFDRHPGVFAHIL CIKD_HUMAN 55 55 -
FFFDRHPGVFAHIL CIKD_RAT 55 55 -
FFFDRHPGVFAYVL CIKF_HUMAN 135 135 -
FFFDRHPGVFAYVL CIKG_HUMAN 94 94 -
FFFDRHPGVFAYVL CIKE_RAT 102 102 -
YFFDRHPGVFAQVL Q26041 48 48 -

Motif 2 width=16
Element Seqn Id St Int Rpt
YYRTGKLHCPADVCGP CIKD_HUMAN 70 1 -
YYRTGKLHCPADVCGP CIKD_RAT 70 1 -
YYRTGKLHCPADVCGP CIKF_HUMAN 150 1 -
YYRTGKLHCPADVCGP CIKG_HUMAN 109 1 -
YYRTGKLHCPADVCGP CIKE_RAT 117 1 -
YYRTGKLHYPTDVCGP Q26041 63 1 -

Motif 3 width=22
Element Seqn Id St Int Rpt
EEELAFWGIDETDVEPCCWMTY CIKD_HUMAN 88 2 -
EEELAFWGIDETDVEPCCWMTY CIKD_RAT 88 2 -
EEELGFWGIDETDVEACCWMTY CIKF_HUMAN 168 2 -
EEELTFWGIDETDVEPCCWMTY CIKG_HUMAN 127 2 -
EEELAFWGIDETDVEPCCWMTY CIKE_RAT 135 2 -
EEELEYWGLDSNQVEPCCWMTY Q26041 81 2 -

Motif 4 width=13
Element Seqn Id St Int Rpt
FEDPYSSRYARYV CIKD_HUMAN 180 70 -
FEDPYSSRYARYV CIKD_RAT 180 70 -
FEDPYSSRAARYV CIKF_HUMAN 280 90 -
FEDPYSSRAARVV CIKG_HUMAN 216 67 -
FEDPYSSRAARFI CIKE_RAT 219 62 -
FDEPYSSQAAKVI Q26041 159 56 -

Motif 5 width=15
Element Seqn Id St Int Rpt
KQKLPKKKKKHIPRP CIKD_HUMAN 449 256 -
KQKLPKKKKKHIPRP CIKD_RAT 449 256 -
KQKLPKKKNKHIPRP CIKF_HUMAN 552 259 -
KQKLPKKRKKHVPRP CIKG_HUMAN 485 256 -
KQKLPRKRKKHIPPA CIKE_RAT 486 254 -
RAKLPKKRRRVLPVE Q26041 421 249 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
FFFDRHPGVFAHIL CIKD_HUMAN 55 55 -
FFFDRHPGVFAHIL CIKD_MOUSE 55 55 -
FFFDRHPGVFAHIL CIKD_RAT 55 55 -
FFFDRHPGVFAHIL Q9XSJ8 55 55 -
FFFDRHPGVFAYVL CIKF_HUMAN 135 135 -
FFFDRHPGVFAYVL CIKF_MOUSE 136 136 -
FFFDRHPGVFAYVL CIKF_RAT 137 137 -
FFFDRHPGVFAYVL CIKG_HUMAN 94 94 -
FFFDRHPGVFAYVL CIKG_RAT 95 95 -
FFFDRHPGVFAYVL CIKE_RAT 102 102 -
FFFDRHPQVFACVL Q9PVD1 55 55 -
YFFDRHPGVFAQVL CIKW_DROME 53 53 -
YFFDRHPGVFAQVL Q26041 48 48 -
YFFDRHPGVFAQIL O76457 53 53 -
YFFDRHPGVFTQIL Q9VLC6 55 55 -
YFFDRHPGVFSMIL Q19464 48 48 -
YFFDRHPAVFAMIL O62350 80 80 -
YFFDRHPGVFAQIL Q22012 48 48 -

Motif 2 width=16
Element Seqn Id St Int Rpt
YYRTGKLHCPADVCGP CIKD_HUMAN 70 1 -
YYRTGKLHCPADVCGP CIKD_MOUSE 70 1 -
YYRTGKLHCPADVCGP CIKD_RAT 70 1 -
YYRTGKLHCPADVCGP Q9XSJ8 70 1 -
YYRTGKLHCPADVCGP CIKF_HUMAN 150 1 -
YYRTGKLHCPADVCGP CIKF_MOUSE 151 1 -
YYRTGKLHCPADVCGP CIKF_RAT 152 1 -
YYRTGKLHCPADVCGP CIKG_HUMAN 109 1 -
YYRTGKLHCPADVCGP CIKG_RAT 110 1 -
YYRTGKLHCPADVCGP CIKE_RAT 117 1 -
YYRTGKLHCPSDVCGP Q9PVD1 70 1 -
YYRTGKLHYPTDVCGP CIKW_DROME 68 1 -
YYRTGKLHYPTDVCGP Q26041 63 1 -
YYRSGKLHYPTDVCGP O76457 68 1 -
YYRTGKLHYPTDVCGP Q9VLC6 70 1 -
YYRTGKLHYPTNVCGP Q19464 63 1 -
YYRTGKLHYPTDVCGP O62350 95 1 -
YYRTGKLHYPLDVCGP Q22012 63 1 -

Motif 3 width=22
Element Seqn Id St Int Rpt
EEELAFWGIDETDVEPCCWMTY CIKD_HUMAN 88 2 -
EEELAFWGIDETDVEPCCWMTY CIKD_MOUSE 88 2 -
EEELAFWGIDETDVEPCCWMTY CIKD_RAT 88 2 -
EEELAFWGIDETDVEPCCWMTY Q9XSJ8 88 2 -
EEELGFWGIDETDVEACCWMTY CIKF_HUMAN 168 2 -
EEELGFWGIDETDVEACCWMTY CIKF_MOUSE 169 2 -
EEELGFWGIDETDVEACCWMTY CIKF_RAT 170 2 -
EEELTFWGIDETDVEPCCWMTY CIKG_HUMAN 127 2 -
EEELTFWGIDETDVEPCCWMTY CIKG_RAT 128 2 -
EEELAFWGIDETDVEPCCWMTY CIKE_RAT 135 2 -
EEELAFWGIDETDVEACCWMNY Q9PVD1 88 2 -
EEELEFWGLDSNQVEPCCWMTY CIKW_DROME 86 2 -
EEELEYWGLDSNQVEPCCWMTY Q26041 81 2 -
EEELEFWGLDSNQVEPCCWMTY O76457 86 2 -
EEELEFWGLDSNQVEPCCWSTY Q9VLC6 88 2 -
EEELEFWGLDANQVEPCCWMTY Q19464 81 2 -
EEELQYWGLDASDTEPCCWMQL O62350 113 2 -
EEELKYWGLDSNECEPCCWMTL Q22012 81 2 -

Motif 4 width=13
Element Seqn Id St Int Rpt
FEDPYSSRYARYV CIKD_HUMAN 180 70 -
FEDPYSSRYARYV CIKD_MOUSE 180 70 -
FEDPYSSRYARYV CIKD_RAT 180 70 -
FEDPYSSRYARYV Q9XSJ8 180 70 -
FEDPYSSRAARYV CIKF_HUMAN 280 90 -
FEDPYSSRAARYV CIKF_MOUSE 280 89 -
FEDPYSSRAARYV CIKF_RAT 281 89 -
FEDPYSSRAARVV CIKG_HUMAN 216 67 -
FEDPYSSRAARVV CIKG_RAT 217 67 -
FEDPYSSRAARFI CIKE_RAT 219 62 -
FEDPYSSKYARYI Q9PVD1 161 51 -
FDEPYSSNAAKTI CIKW_DROME 164 56 -
FDEPYSSQAAKVI Q26041 159 56 -
FDEPYSSTAAKII O76457 164 56 -
FDEPSSSTGAKIV Q9VLC6 166 56 -
FDEPWSSKYARVI Q19464 159 56 -
FDEPYSSQAAKLI O62350 194 59 -
FDEPNSSRSAQFI Q22012 159 56 -

Motif 5 width=15
Element Seqn Id St Int Rpt
KQKLPKKKKKHIPRP CIKD_HUMAN 449 256 -
KQKLPKKKKKHIPRP CIKD_MOUSE 449 256 -
KQKLPKKKKKHIPRP CIKD_RAT 449 256 -
KQKLPKKKKKHIPRP Q9XSJ8 449 256 -
KQKLPKKKNKHIPRP CIKF_HUMAN 552 259 -
KQKLPKKKNKHIPRP CIKF_MOUSE 552 259 -
KQKLPKKKNKHIPRP CIKF_RAT 553 259 -
KQKLPKKRKKHVPRP CIKG_HUMAN 485 256 -
KQKLPKKRKKHVPRP CIKG_RAT 486 256 -
KQKLPRKRKKHIPPA CIKE_RAT 486 254 -
KQKLPKKKNKHIPRP Q9PVD1 430 256 -
RAKLPKKRRRVLPVE CIKW_DROME 426 249 -
RAKLPKKRRRVLPVE Q26041 421 249 -
RSKLPKKRRRVLPVE O76457 423 246 -
RSKLPKKRRRVLPVE Q9VLC6 417 238 -
RAKLPKKRRRVLQVI Q19464 428 256 -
RDKLPKRRRRVLPVE O62350 455 248 -
RSKMPKKRRGVLSMD Q22012 425 253 -