WORKLIST ENTRIES (1):
KV31CHANNEL View alignment Kv3.1 voltage-gated K+ channel signature
Type of fingerprint: COMPOUND with 4 elements
Links:
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01495 SHABCHANNEL
PRINTS; PR01496 SHAKERCHANEL; PR01497 SHALCHANNEL; PR01492 KV6CHANNEL
PRINTS; PR01493 KV8CHANNEL; PR01494 KV9CHANNEL; PR01498 SHAWCHANNEL
PRINTS; PR01582 KV34CHANNEL; PR01583 KV33CHANNEL
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].
Kv3.1 channels have slow-rising delayed rectifier-type outward currents that
inactivate slowly. They have a tentative role in the fast action potential
repolarisation abundant in rapidly firing neurons, such as the auditory
brainstem, and hippocampal and cortical interneurons [4]. There are two
forms, -a and -b, which differ in expression during development. Kv3.1a
appears to be found in the neurons of the adult brain, whereas Kv3.1b is
expressed in embryonic and perinatal neurons. In addition, Kv3.1 channels
can also be found in T-lymphocytes [4].
KV31CHANNEL is a 4-element fingerprint that provides a signature for the
Kv3.1 voltage-gated K+ channel. The fingerprint was derived from an initial
alignment of 4 sequences: the motifs were drawn from conserved regions
spanning the full alignment length - motif 1 is situated in the N-terminus;
motifs 2 and 3 lie in the loop between the first and second putative TM
domains; and motif 4 is located 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. Several partial matches were
found, all of which are members of the Kv3.1 channel family or are
closely related K+ channels that fail to make significant matches with
one or more motifs.
SUMMARY INFORMATION
4 codes involving 4 elements
2 codes involving 3 elements
4 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
4| 4 4 4 4
3| 0 2 2 2
2| 0 4 0 4
--+---------------------
| 1 2 3 4
True positives..
CIKD_HUMAN CIKD_RAT CIKD_MOUSE Q9XSJ8
Subfamily: Codes involving 3 elements
Subfamily True positives..
Q9PVD1 CIKG_RAT
Subfamily: Codes involving 2 elements
Subfamily True positives..
Q9IA29 CIKE_RAT CIKG_HUMAN Q9H1V7
PROTEIN TITLES
CIKD_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) -
CIKD_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) (
CIKD_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.1 (KV4) (NGK2) -
Q9XSJ8 KV3.1 - Canis familiaris (Dog).
Q9PVD1 KV3.1 POTASSIUM CHANNEL - Xenopus laevis (African clawed fro
CIKG_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (RAW3) - Rattu
Q9IA29 SHAW-RELATED POTASSIUM CHANNEL PROTEIN RAW1 - Oncorhynchus m
CIKE_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.2 (KSHIIIA) - Ra
CIKG_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (KSHIIIC) - Ho
Q9H1V7 DJ1003J2.3.1 (POTASSIUM VOLTAGE-GATED CHANNEL, SHAW-RELATED
SCAN HISTORY
SPTR39.22_17.3f 1 50 NSINGLE
INITIAL MOTIF SETS
KV31CHANNEL1 Length of motif = 9 Motif number = 1
Kv3.1 voltage-gated K+ channel motif I - 1
PCODE ST INT
GPGDSGDGE CIKD_HUMAN 138 138
GPGDSGDGE CIKD_RAT 138 138
GPGDSGDGE CIKD_MOUSE 138 138
GPGDSGDGE Q9XSJ8 138 138
KV31CHANNEL2 Length of motif = 16 Motif number = 2
Kv3.1 voltage-gated K+ channel motif II - 1
PCODE ST INT
HERFNPIVNKTEIENV CIKD_HUMAN 212 65
HERFNPIVNKTEIENV CIKD_RAT 212 65
HERFNPIVNKTEIENV CIKD_MOUSE 212 65
HERFNPIVNKTEIENV Q9XSJ8 212 65
KV31CHANNEL3 Length of motif = 13 Motif number = 3
Kv3.1 voltage-gated K+ channel motif III - 1
PCODE ST INT
RNGTQVRYYREAE CIKD_HUMAN 228 0
RNGTQVRYYREAE CIKD_RAT 228 0
RNGTQVRYYREAE CIKD_MOUSE 228 0
RNDTQVRYYREAE Q9XSJ8 228 0
KV31CHANNEL4 Length of motif = 15 Motif number = 4
Kv3.1 voltage-gated K+ channel motif IV - 1
PCODE ST INT
VVNSPHHSTQSDTCP CIKD_HUMAN 475 234
VVNSPHHSTQSDTCP CIKD_RAT 475 234
VVNSPHHSTQSDTCP CIKD_MOUSE 475 234
VVNSPHHSTQSDTCP Q9XSJ8 475 234
FINAL MOTIF SETS
KV31CHANNEL1 Length of motif = 9 Motif number = 1
Kv3.1 voltage-gated K+ channel motif I - 1
PCODE ST INT
GPGDSGDGE CIKD_HUMAN 138 138
GPGDSGDGE CIKD_RAT 138 138
GPGDSGDGE CIKD_MOUSE 138 138
GPGDSGDGE Q9XSJ8 138 138
KV31CHANNEL2 Length of motif = 16 Motif number = 2
Kv3.1 voltage-gated K+ channel motif II - 1
PCODE ST INT
HERFNPIVNKTEIENV CIKD_HUMAN 212 65
HERFNPIVNKTEIENV CIKD_RAT 212 65
HERFNPIVNKTEIENV CIKD_MOUSE 212 65
HERFNPIVNKTEIENV Q9XSJ8 212 65
KV31CHANNEL3 Length of motif = 13 Motif number = 3
Kv3.1 voltage-gated K+ channel motif III - 1
PCODE ST INT
RNGTQVRYYREAE CIKD_HUMAN 228 0
RNGTQVRYYREAE CIKD_RAT 228 0
RNGTQVRYYREAE CIKD_MOUSE 228 0
RNDTQVRYYREAE Q9XSJ8 228 0
KV31CHANNEL4 Length of motif = 15 Motif number = 4
Kv3.1 voltage-gated K+ channel motif IV - 1
PCODE ST INT
VVNSPHHSTQSDTCP CIKD_HUMAN 475 234
VVNSPHHSTQSDTCP CIKD_RAT 475 234
VVNSPHHSTQSDTCP CIKD_MOUSE 475 234
VVNSPHHSTQSDTCP Q9XSJ8 475 234
User query: Display/Full Code "KV31CHANNEL"