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PR01495

Identifier
SHABCHANNEL  [View Relations]  [View Alignment]  
Accession
PR01495
No. of Motifs
6
Creation Date
12-MAR-2001
Title
Shab voltage-gated K+ channel family signature
Database References
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01514 KV21CHANNEL
PRINTS; PR01515 KV22CHANNEL
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.
Shab.
IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.524-558.

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 Shab voltage-gated delayed rectifier K+ channels (also known as Kv2 
channels) are responsible for much of the delayed rectifier current in 
Drosophila nervous system and muscle. However, in vertebrates, Kv2 channels
have largely undetermined roles in the delayed rectifier currents of the 
heart and skeletal muscle. Kv2 channels can be further divided into 2
subtypes, designated Kv2.1 and Kv2.2 [4].
 
SHABCHANNEL is a 6-element fingerprint that provides a signature for the
Shab voltage-gated K+ channel family. The fingerprint was derived from an
initial alignment of 5 sequences: the motifs were drawn from conserved
regions spanning the full alignment length: motifs 1 and 2 reside within the
N-terminus; motif 3 spans the loop between putative TM domains 2 and 3;
motif 4 lies in TM domain 6; and motifs 5 and 6 reside at the C-terminus.
Four iterations on SPTR39_15f were required to reach convergence, at which
point a true set comprising 19 sequences was identified. 
Summary Information
19 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 Feature Index
6191919191919
5000000
4000000
3000000
2000000
123456
True Positives
CIKA_HUMAN    CIKA_RAT      CIKB_CANFA    CIKB_DROME    
CIKB_HUMAN CIKB_RAT O18476 O18868
O76805 O97045 Q03717 Q14193
Q26344 Q91592 Q91593 Q9I7T9
Q9I7U0 Q9MZ19 Q9QUU4
Sequence Titles
CIKA_HUMAN  VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.1 (DHK1) - Homo sapiens (Human). 
CIKA_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.1 (DRK1) - Rattus norvegicus (Rat).
CIKB_CANFA DELAYED RECTIFIER POTASSIUM CHANNEL PROTEIN - CANIS FAMILIARIS (DOG).
CIKB_DROME VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN SHAB (SHAB11) - Drosophila melanogaster (Fruit fly).
CIKB_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.2 - Homo sapiens (Human).
CIKB_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.2 (CDRK) - Rattus norvegicus (Rat).
O18476 KV2 VOLTAGE-GATED POTASSIUM CHANNEL - Loligo pealeii (Longfin squid).
O18868 DELAYED RECTIFIER POTASSIUM CHANNEL KV2.1 - Sus scrofa (Pig).
O76805 DELAYED RECTIFIER POTASSIUM CHANNEL - Drosophila melanogaster (Fruit fly).
O97045 KV2 CHANNEL ALPHA-SUBUNIT - Halocynthia roretzi (Sea squirt).
Q03717 POTASSIUM CHANNEL PROTEIN - Mus musculus (Mouse).
Q14193 H-DRK1 K(+) CHANNEL (DJ791K14.1) (POTASSIUM VOLTAGE-GATED CHANNEL, SHAB-RELATED SUBFAMILY, MEMBER 1) - Homo sapiens (Human).
Q26344 ACTION POTENTIAL BROADENING POTASSIUM CHANNEL - Aplysia sp. (Sea hare).
Q91592 POTASSIUM CHANNEL ALPHA SUBUNIT KV2.2 - Xenopus laevis (African clawed frog).
Q91593 POTASSIUM CHANNEL ALPHA SUBUNIT KV2.1 - Xenopus laevis (African clawed frog).
Q9I7T9 SHAB PROTEIN - Drosophila melanogaster (Fruit fly).
Q9I7U0 SHAB PROTEIN - Drosophila melanogaster (Fruit fly).
Q9MZ19 VOLTAGE-GATED POTASSIUM CHANNEL KV2.1 - Oryctolagus cuniculus (Rabbit).
Q9QUU4 K+ CHANNEL, DRK1 - Rattus sp.
Scan History
SPTR39_15f 4  20   NSINGLE    
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
ESCCQARYHQKKEQ CIKA_HUMAN 126 126 -
ESCCQARYHQKKEQ CIKA_RAT 126 126 -
ESCCQARYHQKKEQ CIKB_RAT 134 134 -
ESCCQARYHQKKEQ CIKB_CANFA 134 134 -
ESCCQGRYHQKKEQ O97045 169 169 -

Motif 2 width=15
Element Seqn Id St Int Rpt
NTCCAEKRKKLWDLL CIKA_HUMAN 161 21 -
NTCCAEKRKKLWDLL CIKA_RAT 161 21 -
NTCCPEKRKKLWDLL CIKB_RAT 169 21 -
NTCCPEKRKKSRDLL CIKB_CANFA 169 21 -
GMCCAQKRKKLWDLL O97045 204 21 -

Motif 3 width=14
Element Seqn Id St Int Rpt
KKWKFFKGPLNAID CIKA_HUMAN 249 73 -
KKWKFFKGPLNAID CIKA_RAT 249 73 -
NKWKFFKGPLNVID CIKB_RAT 257 73 -
NKWKFFKGPLNVID CIKB_CANFA 257 73 -
NKWKFFKGPLNIID O97045 288 69 -

Motif 4 width=12
Element Seqn Id St Int Rpt
GGLCCIAGVLVI CIKA_HUMAN 390 127 -
GGLCCIAGVLVI CIKA_RAT 390 127 -
GGLCCIAGVLVI CIKB_RAT 398 127 -
GGLCCIAGVLVI CIKB_CANFA 398 127 -
GATCCITGVLVI O97045 429 127 -

Motif 5 width=12
Element Seqn Id St Int Rpt
SEFYKEQKRQEK CIKA_HUMAN 413 11 -
SEFYKEQKRQEK CIKA_RAT 413 11 -
SEFYKEQKRQEK CIKB_RAT 421 11 -
SEFYKEQKRQEK CIKB_CANFA 421 11 -
SEFYKEQKRQEK O97045 452 11 -

Motif 6 width=16
Element Seqn Id St Int Rpt
KDAFARSIEMMDIVVE CIKA_HUMAN 447 22 -
KDAFARSIEMMDIVVE CIKA_RAT 447 22 -
KDAFARSMELIDVAVE CIKB_RAT 455 22 -
KDAFARSMELIDVAVE CIKB_CANFA 455 22 -
RDVYAKSLELVDVTKS O97045 486 22 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
ESCCQARYHQKKEQ CIKA_HUMAN 126 126 -
ESCCQARYHQKKEQ CIKA_RAT 126 126 -
ESCCQARYHQKKEQ Q03717 130 130 -
ESCCQARYHQKKEQ Q14193 130 130 -
ESCCQARYHQKKEQ Q9QUU4 130 130 -
ESCCQARYHQKKEQ Q9MZ19 130 130 -
ESCCQARYHQKKEQ CIKB_RAT 134 134 -
ESCCQARYHQKKEQ Q91593 130 130 -
ESCCQARYHQKKEQ CIKB_HUMAN 134 134 -
ESCCQARYHQKKEQ O18868 130 130 -
ESCCQARYHQKKEQ Q91592 134 134 -
ESCCQARYHQKKEQ CIKB_CANFA 134 134 -
ESCCQGRYHQKKEQ O97045 169 169 -
ESCCQHKYHQRKEN Q9I7T9 406 406 -
ESCCQHKYHQRKEN Q9I7U0 406 406 -
ESCCQHKYHQRKEN CIKB_DROME 376 376 -
ESCCQHKYHQRKEN O76805 376 376 -
ESCCQHRYHQKKEH Q26344 256 256 -
ESCCQHKYHQKKEH O18476 322 322 -

Motif 2 width=15
Element Seqn Id St Int Rpt
NTCCAEKRKKLWDLL CIKA_HUMAN 161 21 -
NTCCAEKRKKLWDLL CIKA_RAT 161 21 -
NTCCAEKRKKLWDLL Q03717 165 21 -
NTCCAEKRKKLWDLL Q14193 165 21 -
NTCCAEKRKKLWDLL Q9QUU4 165 21 -
NTCCAEKRKKLWDLL Q9MZ19 165 21 -
NTCCPEKRKKLWDLL CIKB_RAT 169 21 -
NTCCADKRKKLWDLL Q91593 165 21 -
NTCCPDKRKKLWDLL CIKB_HUMAN 169 21 -
NTCCAEKRKKLWDLL O18868 165 21 -
NTCCPEKTKKLWDLL Q91592 169 21 -
NTCCPEKRKKSRDLL CIKB_CANFA 169 21 -
GMCCAQKRKKLWDLL O97045 204 21 -
EGKCAEYQKYLWELL Q9I7T9 441 21 -
EGKCAEYQKYLWELL Q9I7U0 441 21 -
EGKFSEYQKYLWELL CIKB_DROME 411 21 -
EGKFSEYQKYLWELL O76805 411 21 -
TGVCSHWRQKVWDLL Q26344 291 21 -
TGSFAKWRQRVWDLL O18476 357 21 -

Motif 3 width=14
Element Seqn Id St Int Rpt
KKWKFFKGPLNAID CIKA_HUMAN 249 73 -
KKWKFFKGPLNAID CIKA_RAT 249 73 -
KKWKFFKGPLNAID Q03717 253 73 -
KKWKFFKGPLNAID Q14193 253 73 -
KKWKFFKGPLNAID Q9QUU4 253 73 -
KKWKFFKGPLNAID Q9MZ19 253 73 -
NKWKFFKGPLNVID CIKB_RAT 257 73 -
NKWKFFKGPLNVID Q91593 253 73 -
NKWKFFKGPLNVID CIKB_HUMAN 257 73 -
KKWKFFKGPLNAID O18868 253 73 -
NKWKFFKGPLNIID Q91592 257 73 -
NKWKFFKGPLNVID CIKB_CANFA 257 73 -
NKWKFFKGPLNIID O97045 288 69 -
DKWKFFKGGLNIID Q9I7T9 532 76 -
DKWKFFKGGLNIID Q9I7U0 528 72 -
DKWKFFKGGLNIID CIKB_DROME 498 72 -
DKWKFFKGGLNIID O76805 498 72 -
NKWKFFKGPLNVID Q26344 379 73 -
NKWKFFKGPLNIID O18476 444 72 -

Motif 4 width=12
Element Seqn Id St Int Rpt
GGLCCIAGVLVI CIKA_HUMAN 390 127 -
GGLCCIAGVLVI CIKA_RAT 390 127 -
GGLCCIAGVLVI Q03717 394 127 -
GGLCCIAGVLVI Q14193 394 127 -
GGLCCIAGVLVI Q9QUU4 394 127 -
GGLCCIAGVLVI Q9MZ19 394 127 -
GGLCCIAGVLVI CIKB_RAT 398 127 -
GGLCCIAGVLVI Q91593 394 127 -
GGLCCIAGVLVI CIKB_HUMAN 398 127 -
GGLCCIAGVLVI O18868 394 127 -
GGLCCIAGVLVI Q91592 398 127 -
GGLCCIAGVLVI CIKB_CANFA 398 127 -
GATCCITGVLVI O97045 429 127 -
GTVCCICGVLVI Q9I7T9 674 128 -
GTVCCICGVLVI Q9I7U0 670 128 -
GTVCCICGVLVV CIKB_DROME 640 128 -
GTVCCICGVLVV O76805 640 128 -
GSVCCICGVLVI Q26344 521 128 -
GGVCCICGVLVV O18476 586 128 -

Motif 5 width=12
Element Seqn Id St Int Rpt
SEFYKEQKRQEK CIKA_HUMAN 413 11 -
SEFYKEQKRQEK CIKA_RAT 413 11 -
SEFYKEQKRQEK Q03717 417 11 -
SEFYKEQKRQEK Q14193 417 11 -
SEFYKEQKRQEK Q9QUU4 417 11 -
SEFYKEQKRQEK Q9MZ19 417 11 -
SEFYKEQKRQEK CIKB_RAT 421 11 -
SEFYKEQKRQEK Q91593 417 11 -
SEFYKEQKRQEK CIKB_HUMAN 421 11 -
SEFYKEQKRQEK O18868 417 11 -
SEFYKEQKRQEK Q91592 421 11 -
SEFYKEQKRQEK CIKB_CANFA 421 11 -
SEFYKEQKRQEK O97045 452 11 -
AEFYKNQMRREK Q9I7T9 697 11 -
AEFYKNQMRREK Q9I7U0 693 11 -
AEFYKNQMRREK CIKB_DROME 663 11 -
AEFYKNQMRREK O76805 663 11 -
AEFYKDQMRREK Q26344 544 11 -
AEFYKDQMRREK O18476 609 11 -

Motif 6 width=16
Element Seqn Id St Int Rpt
KDAFARSIEMMDIVVE CIKA_HUMAN 447 22 -
KDAFARSIEMMDIVVE CIKA_RAT 447 22 -
KDAFARSIEMMDIVVE Q03717 451 22 -
KDAFARSIEMMDIVVE Q14193 451 22 -
KDAFARSIEMMDIVVE Q9QUU4 451 22 -
KDAFARSVEMMDIVVE Q9MZ19 451 22 -
KDAFARSMELIDVAVE CIKB_RAT 455 22 -
KDAFARSVELMDVVVE Q91593 451 22 -
KDAFARSMELIDVAVE CIKB_HUMAN 455 22 -
KDAFPRSIEMMDIVVE O18868 451 22 -
KDAFARSMELIDIAVD Q91592 455 22 -
KDAFARSMELIDVAVE CIKB_CANFA 455 22 -
RDVYAKSLELVDVTKS O97045 486 22 -
KDAFAKSMDLIDVIVD Q9I7T9 734 25 -
KDAFAKSMDLIDVIVD Q9I7U0 730 25 -
KDAFAKSMDLIDVIVD CIKB_DROME 700 25 -
KDAFAKSMDLIDVIVD O76805 700 25 -
RDAFARSVDLMEVNSP Q26344 581 25 -
RDAFAKSVDLMDVASE O18476 646 25 -