WORKLIST ENTRIES (1):
SHAWCHANNEL View alignment View Structure Shaw voltage-gated K+ channel family signature
Type of fingerprint: COMPOUND with 5 elements
Links:
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01495 SHABCHANNEL
PRINTS; PR01496 SHAKERCHANEL; PR01497 SHALCHANNEL; PR01492 KV6CHANNEL
PRINTS; PR01493 KV8CHANNEL; PR01494 KV9CHANNEL
PRINTS; PR01581 KV31CHANNEL; PR01582 KV33CHANNEL; PR01583 KV34CHANNEL
Creation date 26-FEB-2001
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.
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 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 FINGERPRINT INDEX
5| 18 18 18 18 18
4| 0 0 0 0 0
3| 0 0 0 0 0
2| 0 0 0 0 0
--+--------------------------
| 1 2 3 4 5
True positives..
CIKD_HUMAN CIKD_MOUSE CIKD_RAT Q9XSJ8
CIKF_HUMAN CIKF_MOUSE CIKF_RAT CIKG_RAT
CIKG_HUMAN CIKE_RAT Q9PVD1 CIKW_DROME
Q26041 O76457 Q9VLC6 Q19464
O62350 Q22012
PROTEIN TITLES
CIKD_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) -
CIKD_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) -
CIKD_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) (
Q9XSJ8 KV3.1 - Canis familiaris (Dog).
CIKF_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Ho
CIKF_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Mu
CIKF_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Ra
CIKG_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (RAW3) - Rattu
CIKG_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (KSHIIIC) - Ho
CIKE_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.2 (KSHIIIA) - Ra
Q9PVD1 KV3.1 POTASSIUM CHANNEL - Xenopus laevis (African clawed fro
CIKW_DROME VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN SHAW (SHAW2) - Droso
Q26041 SHAW POTASSIUM CHANNEL - Panulirus interruptus (California s
O76457 SHAW POTASSIUM CHANNEL KV3.1A - Aplysia californica (Califor
Q9VLC6 CG4450 PROTEIN - Drosophila melanogaster (Fruit fly).
Q19464 F14F11.1 PROTEIN - Caenorhabditis elegans.
O62350 EGL-36 PROTEIN - Caenorhabditis elegans.
Q22012 R186.5 PROTEIN - Caenorhabditis elegans.
SCAN HISTORY
SPTR39_14f 3 20 NSINGLE
INITIAL MOTIF SETS
SHAWCHANNEL1 Length of motif = 14 Motif number = 1
Shaw voltage-gated K+ channel family motif I - 1
PCODE ST INT
FFFDRHPGVFAHIL CIKD_HUMAN 55 55
FFFDRHPGVFAHIL CIKD_RAT 55 55
FFFDRHPGVFAYVL CIKF_HUMAN 135 135
FFFDRHPGVFAYVL CIKE_RAT 102 102
FFFDRHPGVFAYVL CIKG_HUMAN 94 94
YFFDRHPGVFAQVL Q26041 48 48
SHAWCHANNEL2 Length of motif = 16 Motif number = 2
Shaw voltage-gated K+ channel family motif II - 1
PCODE ST INT
YYRTGKLHCPADVCGP CIKD_HUMAN 70 1
YYRTGKLHCPADVCGP CIKD_RAT 70 1
YYRTGKLHCPADVCGP CIKF_HUMAN 150 1
YYRTGKLHCPADVCGP CIKE_RAT 117 1
YYRTGKLHCPADVCGP CIKG_HUMAN 109 1
YYRTGKLHYPTDVCGP Q26041 63 1
SHAWCHANNEL3 Length of motif = 22 Motif number = 3
Shaw voltage-gated K+ channel family motif III - 1
PCODE ST INT
EEELAFWGIDETDVEPCCWMTY CIKD_HUMAN 88 2
EEELAFWGIDETDVEPCCWMTY CIKD_RAT 88 2
EEELGFWGIDETDVEACCWMTY CIKF_HUMAN 168 2
EEELAFWGIDETDVEPCCWMTY CIKE_RAT 135 2
EEELTFWGIDETDVEPCCWMTY CIKG_HUMAN 127 2
EEELEYWGLDSNQVEPCCWMTY Q26041 81 2
SHAWCHANNEL4 Length of motif = 13 Motif number = 4
Shaw voltage-gated K+ channel family motif IV - 1
PCODE ST INT
FEDPYSSRYARYV CIKD_HUMAN 180 70
FEDPYSSRYARYV CIKD_RAT 180 70
FEDPYSSRAARYV CIKF_HUMAN 280 90
FEDPYSSRAARFI CIKE_RAT 219 62
FEDPYSSRAARVV CIKG_HUMAN 216 67
FDEPYSSQAAKVI Q26041 159 56
SHAWCHANNEL5 Length of motif = 15 Motif number = 5
Shaw voltage-gated K+ channel family motif V - 1
PCODE ST INT
KQKLPKKKKKHIPRP CIKD_HUMAN 449 256
KQKLPKKKKKHIPRP CIKD_RAT 449 256
KQKLPKKKNKHIPRP CIKF_HUMAN 552 259
KQKLPRKRKKHIPPA CIKE_RAT 486 254
KQKLPKKRKKHVPRP CIKG_HUMAN 485 256
RAKLPKKRRRVLPVE Q26041 421 249
FINAL MOTIF SETS
SHAWCHANNEL1 Length of motif = 14 Motif number = 1
Shaw voltage-gated K+ channel family motif I - 3
PCODE ST INT
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
SHAWCHANNEL2 Length of motif = 16 Motif number = 2
Shaw voltage-gated K+ channel family motif II - 3
PCODE ST INT
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
SHAWCHANNEL3 Length of motif = 22 Motif number = 3
Shaw voltage-gated K+ channel family motif III - 3
PCODE ST INT
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
SHAWCHANNEL4 Length of motif = 13 Motif number = 4
Shaw voltage-gated K+ channel family motif IV - 3
PCODE ST INT
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
SHAWCHANNEL5 Length of motif = 15 Motif number = 5
Shaw voltage-gated K+ channel family motif V - 3
PCODE ST INT
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
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