WORKLIST ENTRIES (1):
KV33CHANNEL View alignment Kv3.3 voltage-gated K+ channel signature
Type of fingerprint: COMPOUND with 6 elements
Links:
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01495 SHABCHANNEL
PRINTS; PR01496 SHAKERCHANEL; PR01497 SHALCHANNEL; PR01492 KV6CHANNEL
PRINTS; PR01493 KV8CHANNEL; PR01494 KV9CHANNEL; PR01498 SHAWCHANNEL
PRINTS; PR01581 KV31CHANNEL; PR01583 KV34CHANNEL
Creation date 11-SEP-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].
Kv3.3 channels are evenly distributed over the soma and proximal apical
dendrites. They have also been found in the lens epithelium, corneal
endothelium, cerebellar cells and the deep cerebellar nuclei. When
co-expressed with NADPH oxidase, they function as an oxygen sensor complex
in airway chemoreceptors [4].
KV33CHANNEL is a 6-element fingerprint that provides a signature for the
Kv3.3 voltage-gated K+ channel. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions
spanning the full alignment length - motifs 1-4 lie in the N-terminus; motif
5 is located in the first putative TM domain; and motif 6 is situated in the
C-terminus. A single iteration on SPTR39.22_17.3f was required to reach
convergence, no further sequences being identified beyond the starting set.
SUMMARY INFORMATION
3 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 FINGERPRINT INDEX
6| 3 3 3 3 3 3
5| 0 0 0 0 0 0
4| 0 0 0 0 0 0
3| 0 0 0 0 0 0
2| 0 0 0 0 0 0
--+-------------------------------
| 1 2 3 4 5 6
True positives..
CIKF_MOUSE CIKF_RAT CIKF_HUMAN
PROTEIN TITLES
CIKF_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Mu
CIKF_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Ra
CIKF_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.3 (KSHIIID) - Ho
SCAN HISTORY
SPTR39.22_17.3f 1 125 NSINGLE
INITIAL MOTIF SETS
KV33CHANNEL1 Length of motif = 15 Motif number = 1
Kv3.3 voltage-gated K+ channel motif I - 1
PCODE ST INT
MLSSVCVSSFRGRQG CIKF_HUMAN 1 1
MLSSVCVWSFRGCQG CIKF_MOUSE 1 1
MLSSVCVWSFSGRQG CIKF_RAT 1 1
KV33CHANNEL2 Length of motif = 15 Motif number = 2
Kv3.3 voltage-gated K+ channel motif II - 1
PCODE ST INT
RGPGGRRAEPCPGLP CIKF_HUMAN 59 43
LRPGGRRAEPCPGLP CIKF_MOUSE 60 44
CGPGGRRAEPCSGLP CIKF_RAT 61 45
KV33CHANNEL3 Length of motif = 14 Motif number = 3
Kv3.3 voltage-gated K+ channel motif III - 1
PCODE ST INT
ANAAGAHDGGLDDE CIKF_HUMAN 214 140
ANAGGAHDAGLDDE CIKF_MOUSE 214 139
ANAGGAHDAGLDDE CIKF_RAT 215 139
KV33CHANNEL4 Length of motif = 16 Motif number = 4
Kv3.3 voltage-gated K+ channel motif IV - 1
PCODE ST INT
GGGGLDGAGGELKRLC CIKF_HUMAN 231 3
GGGGLDGAGGELKRLC CIKF_MOUSE 231 3
GGGGLDGAGGELKRLC CIKF_RAT 232 3
KV33CHANNEL5 Length of motif = 14 Motif number = 5
Kv3.3 voltage-gated K+ channel motif V - 1
PCODE ST INT
TVTQASPIPGAPPE CIKF_HUMAN 322 75
TVTQASPIPGAPPE CIKF_MOUSE 322 75
TVTQASPIPGAPPE CIKF_RAT 323 75
KV33CHANNEL6 Length of motif = 17 Motif number = 6
Kv3.3 voltage-gated K+ channel motif VI - 1
PCODE ST INT
PDPPPPPPPHPHHGSGG CIKF_HUMAN 577 241
PDPPPPPPPHPHHGSGG CIKF_MOUSE 577 241
PDPPPPPPPHPHHGSGG CIKF_RAT 578 241
FINAL MOTIF SETS
KV33CHANNEL1 Length of motif = 15 Motif number = 1
Kv3.3 voltage-gated K+ channel motif I - 1
PCODE ST INT
MLSSVCVWSFRGCQG CIKF_MOUSE 1 1
MLSSVCVWSFSGRQG CIKF_RAT 1 1
MLSSVCVSSFRGRQG CIKF_HUMAN 1 1
KV33CHANNEL2 Length of motif = 15 Motif number = 2
Kv3.3 voltage-gated K+ channel motif II - 1
PCODE ST INT
LRPGGRRAEPCPGLP CIKF_MOUSE 60 44
CGPGGRRAEPCSGLP CIKF_RAT 61 45
RGPGGRRAEPCPGLP CIKF_HUMAN 59 43
KV33CHANNEL3 Length of motif = 14 Motif number = 3
Kv3.3 voltage-gated K+ channel motif III - 1
PCODE ST INT
ANAGGAHDAGLDDE CIKF_MOUSE 214 139
ANAGGAHDAGLDDE CIKF_RAT 215 139
ANAAGAHDGGLDDE CIKF_HUMAN 214 140
KV33CHANNEL4 Length of motif = 16 Motif number = 4
Kv3.3 voltage-gated K+ channel motif IV - 1
PCODE ST INT
GGGGLDGAGGELKRLC CIKF_MOUSE 231 3
GGGGLDGAGGELKRLC CIKF_RAT 232 3
GGGGLDGAGGELKRLC CIKF_HUMAN 231 3
KV33CHANNEL5 Length of motif = 14 Motif number = 5
Kv3.3 voltage-gated K+ channel motif V - 1
PCODE ST INT
TVTQASPIPGAPPE CIKF_MOUSE 322 75
TVTQASPIPGAPPE CIKF_RAT 323 75
TVTQASPIPGAPPE CIKF_HUMAN 322 75
KV33CHANNEL6 Length of motif = 17 Motif number = 6
Kv3.3 voltage-gated K+ channel motif VI - 1
PCODE ST INT
PDPPPPPPPHPHHGSGG CIKF_MOUSE 577 241
PDPPPPPPPHPHHGSGG CIKF_RAT 578 241
PDPPPPPPPHPHHGSGG CIKF_HUMAN 577 241
User query: Display/Full Code "KV33CHANNEL"