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

User query: Display/Full Code "SHABCHANNEL"