WORKLIST ENTRIES (1):
SHABCHANNEL View alignment Shab voltage-gated K+ channel family signature
Type of fingerprint: COMPOUND with 6 elements
Links:
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL
PRINTS; PR01496 SHAKERCHANEL; PR01497 SHALCHANNEL; PR01498 SHAWCHANNEL
PRINTS; PR01492 KV6CHANNEL; PR01493 KV8CHANNEL; PR01494 KV9CHANNEL
PRINTS; PR01514 KV21CHANNEL; PR01515 KV22CHANNEL
Creation date 12-MAR-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.
Shab.
IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.524-558.
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 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 FINGERPRINT INDEX
6| 19 19 19 19 19 19
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..
Q9QUU4 Q14193 Q03717 CIKA_RAT
CIKA_HUMAN Q9MZ19 CIKB_RAT Q91593
CIKB_HUMAN O18868 Q91592 CIKB_CANFA
O97045 Q9I7U0 Q9I7T9 CIKB_DROME
O76805 Q26344 O18476
PROTEIN TITLES
Q9QUU4 K+ CHANNEL, DRK1 - Rattus sp.
Q14193 H-DRK1 K(+) CHANNEL (DJ791K14.1) (POTASSIUM VOLTAGE-GATED CH
Q03717 POTASSIUM CHANNEL PROTEIN - Mus musculus (Mouse).
CIKA_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.1 (DRK1) - Rattu
CIKA_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.1 (DHK1) - Homo
Q9MZ19 VOLTAGE-GATED POTASSIUM CHANNEL KV2.1 - Oryctolagus cuniculu
CIKB_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.2 (CDRK) - Rattu
Q91593 POTASSIUM CHANNEL ALPHA SUBUNIT KV2.1 - Xenopus laevis (Afri
CIKB_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.2 - Homo sapiens
O18868 DELAYED RECTIFIER POTASSIUM CHANNEL KV2.1 - Sus scrofa (Pig)
Q91592 POTASSIUM CHANNEL ALPHA SUBUNIT KV2.2 - Xenopus laevis (Afri
CIKB_CANFA VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV2.2 - Canis famili
O97045 KV2 CHANNEL ALPHA-SUBUNIT - Halocynthia roretzi (Sea squirt)
Q9I7U0 SHAB PROTEIN - Drosophila melanogaster (Fruit fly).
Q9I7T9 SHAB PROTEIN - Drosophila melanogaster (Fruit fly).
CIKB_DROME VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN SHAB (SHAB11) - Dros
O76805 DELAYED RECTIFIER POTASSIUM CHANNEL - Drosophila melanogaste
Q26344 ACTION POTENTIAL BROADENING POTASSIUM CHANNEL - Aplysia sp.
O18476 KV2 VOLTAGE-GATED POTASSIUM CHANNEL - Loligo pealeii (Longfi
SCAN HISTORY
SPTR39_15f 4 20 NSINGLE
INITIAL MOTIF SETS
SHABCHANNEL1 Length of motif = 14 Motif number = 1
Shab voltage-gated K+ channel family motif I - 1
PCODE ST INT
ESCCQARYHQKKEQ CIKA_HUMAN 126 126
ESCCQARYHQKKEQ CIKA_RAT 126 126
ESCCQARYHQKKEQ CIKB_CANFA 134 134
ESCCQARYHQKKEQ CIKB_RAT 134 134
ESCCQGRYHQKKEQ O97045 169 169
SHABCHANNEL2 Length of motif = 15 Motif number = 2
Shab voltage-gated K+ channel family motif II - 1
PCODE ST INT
NTCCAEKRKKLWDLL CIKA_HUMAN 161 21
NTCCAEKRKKLWDLL CIKA_RAT 161 21
NTCCPEKRKKSRDLL CIKB_CANFA 169 21
NTCCPEKRKKLWDLL CIKB_RAT 169 21
GMCCAQKRKKLWDLL O97045 204 21
SHABCHANNEL3 Length of motif = 14 Motif number = 3
Shab voltage-gated K+ channel family motif III - 1
PCODE ST INT
KKWKFFKGPLNAID CIKA_HUMAN 249 73
KKWKFFKGPLNAID CIKA_RAT 249 73
NKWKFFKGPLNVID CIKB_CANFA 257 73
NKWKFFKGPLNVID CIKB_RAT 257 73
NKWKFFKGPLNIID O97045 288 69
SHABCHANNEL4 Length of motif = 12 Motif number = 4
Shab voltage-gated K+ channel family motif IV - 1
PCODE ST INT
GGLCCIAGVLVI CIKA_HUMAN 390 127
GGLCCIAGVLVI CIKA_RAT 390 127
GGLCCIAGVLVI CIKB_CANFA 398 127
GGLCCIAGVLVI CIKB_RAT 398 127
GATCCITGVLVI O97045 429 127
SHABCHANNEL5 Length of motif = 12 Motif number = 5
Shab voltage-gated K+ channel family motif V - 1
PCODE ST INT
SEFYKEQKRQEK CIKA_HUMAN 413 11
SEFYKEQKRQEK CIKA_RAT 413 11
SEFYKEQKRQEK CIKB_CANFA 421 11
SEFYKEQKRQEK CIKB_RAT 421 11
SEFYKEQKRQEK O97045 452 11
SHABCHANNEL6 Length of motif = 16 Motif number = 6
Shab voltage-gated K+ channel family motif VI - 1
PCODE ST INT
KDAFARSIEMMDIVVE CIKA_HUMAN 447 22
KDAFARSIEMMDIVVE CIKA_RAT 447 22
KDAFARSMELIDVAVE CIKB_CANFA 455 22
KDAFARSMELIDVAVE CIKB_RAT 455 22
RDVYAKSLELVDVTKS O97045 486 22
FINAL MOTIF SETS
SHABCHANNEL1 Length of motif = 14 Motif number = 1
Shab voltage-gated K+ channel family motif I - 4
PCODE ST INT
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
SHABCHANNEL2 Length of motif = 15 Motif number = 2
Shab voltage-gated K+ channel family motif II - 4
PCODE ST INT
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
SHABCHANNEL3 Length of motif = 14 Motif number = 3
Shab voltage-gated K+ channel family motif III - 4
PCODE ST INT
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
SHABCHANNEL4 Length of motif = 12 Motif number = 4
Shab voltage-gated K+ channel family motif IV - 4
PCODE ST INT
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
SHABCHANNEL5 Length of motif = 12 Motif number = 5
Shab voltage-gated K+ channel family motif V - 4
PCODE ST INT
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
SHABCHANNEL6 Length of motif = 16 Motif number = 6
Shab voltage-gated K+ channel family motif VI - 4
PCODE ST INT
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
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