WORKLIST ENTRIES (1):

RVDCCALPHA1 View alignment      R-type voltage-dependent calcium channel alpha-1 subunit signature
 Type of fingerprint: COMPOUND with 6  elements
Links:
   PRINTS; PR00167 CACHANNEL; PR01629 TVDCCALPHA1; PR01630 LVDCCALPHA1
   PRINTS; PR01631 NVDCCALPHA1; PR01632 PQVDCCALPHA1 

 Creation date 11-DEC-2001

   1. WILLIAMS, M.E., BRUST, P.F., FELDMAN, D.H., PATTHI, S., SIMERSON, S., 
   MAROUFI, A., MCCUE, A.F., VELICELBI, G., ELLIS, S.B. AND HARPOLD, M.M.
   Structure and functional expression of an omega-conotoxin sensitive human
   N-type calcium channel.
   SCIENCE 257 389-395 (1992).

   2. MORI, Y., FRIEDRICH, T., KIM, MS., MIKAMI, A., NAKAI, J., RUTH, P., 
   BOSSE, E., HOFMANN, F., FLOCKERZI, V., FURUICHI, T., MIKOSHIBA, K., 
   IMOTO, K., TANABE, T. AND NUMA, S.
   Primary structure and functional expression from complementary DNA of a 
   brain calcium channel.
   NATURE 350 398-402 (1991).

   3. ASHCROFT, F.M.
   Voltage-gated Ca2+ channels.
   IN ION CHANNELS AND DISEASE, ACADEMIC PRESS, 2000, PP.161-183.

   4. KOCH, W.J., ELLINOR, P.T. AND SCHWARTZ, A.
   cDNA cloning of a dihydropyridine-sensitive calcium channel from rat aorta -
   evidence for the existence of alternatively spliced forms.
   J.BIOL.CHEM. 265(29) 17786-17791 (1990).

   5. RANDALL, A.D. AND TSIEN, R.W.
   Contrasting biophysical and pharmacological properties of T-type and R-type
   calcium channels.
   NEUROPHARMACOLOGY 36(7) 879-893 (1997).

   6. FOEHRING, R.C., MERMELSTEIN, P.G., SONG, W., ULRICH, S. AND SURMEIER, D.J.
   Unique properties of R-type calcium currents in neocortical and neostriatal
   neurons.
   J.NEUROPHYSIOL. 84(5) 2225-2236 (2000).

   7. GASPARINI, S., KASYANOV, A.M., PIETROBON, D., VORONIN, L.L. AND
   CHERUBINI, E.
   Presynaptic R-type calcium channels contribute to fast excitatory synaptic
   transmission in the rat hippocampus.
   J.NEUROSCI. 21(22) 8715-8721 (2001).

   Calcium channel proteins are involved in the control of neurotransmitter
   release from neurons [1], and play an important role in the regulation of a
   variety of cellular functions, including membrane excitability, muscle
   contraction and synaptic transmission [2]. Voltage-gated calcium channels
   are classified as T, L, N, P, Q and R, and are distinguished by their
   sensitivity to pharmacological blocks, single-channel conductance kinetics,
   and voltage-dependence. On the basis of their voltage activation
   properties, the voltage-gated calcium classes can be further divided into
   two broad groups: the low (T-type) and high (L, N, P, Q and R-type)
   threshold-activated channels [3].
   
   Generally, the channel proteins are composed of 4 tightly-coupled subunits
   (alpha-1, alpha-2, beta and gamma), the alpha-1 subunit from each creating
   the pore for the import of extracellular calcium ions. The alpha-1 subunit
   shares sequence characteristics with all voltage-dependent cation channels,
   and exploits the same 6-helix bundle structural motif - in both sodium and
   calcium channels, this motif is repeated 4 times within the sequence to give
   a 24-helix bundle. Within each of these repeats, 5 of the transmembrane (TM)
   segments (S1, S2, S3, S5, S6) are hydrophobic and one is positively charged
   (S4) - the latter is characterised by charged amino acids at very third
   position, and probably represents the voltage-sensor.
  
   Several genes encoding alpha-1 subunits have been identified, each forming
   a distinct electrophysiological channel [4]. R-type calcium channels are
   composed of alpha-1E subunits and are found in a variety of neuronal
   populations, such as cerebellar granule neurons and dendrites of hippocampal
   pyrimidal neurons [5]. They are believed to play an important role in the
   body's natural communication network, where they contribute to the 
   regulation of brain function by synaptic integration [6]. Their hypolarised
   inactivation range and rapid kinetics of inactivation make R-type channels
   more suited to providing a transient surge of Ca2+ influx [6,7].
  
   RVDCCALPHA1 is a 6-element fingerprint that provides a signature for the
   R-type voltage-dependent calcium channel alpha-1 subunit. The fingerprint
   was derived from an initial alignment of 5 sequences: the motifs were drawn
   from conserved regions spanning the N-terminal half of the alignment: motifs
   1 and 2 lie in the extracellular region between TM domains 5 and 6 of repeat
   I; motif 3 resides in the cytoplasmic region between TM domain 6 of repeat I
   and TM domain 1 of repeat II; and motifs 4-6 span the cytoplasmic region 
   between TM domain 6 of repeat II and TM domain 1 of repeat III. A single
   iteration on SPTR40_18f was required to reach convergence, no further 
   sequences being identified beyond the starting set.

  SUMMARY INFORMATION
      5 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|   5    5    5    5    5    5  
    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..
 CCAE_RAT       CCAE_HUMAN     CCAE_MOUSE     CCAE_RABIT     
 CCAE_DISOM     


  PROTEIN TITLES
   CCAE_RAT         Voltage-dependent R-type calcium channel alpha-1E subunit (C
   CCAE_HUMAN       Voltage-dependent R-type calcium channel alpha-1E subunit (C
   CCAE_MOUSE       Voltage-dependent R-type calcium channel alpha-1E subunit (C
   CCAE_RABIT       Voltage-dependent R-type calcium channel alpha-1E subunit (C
   CCAE_DISOM       Probable voltage-dependent R-type calcium channel alpha-1E s

SCAN HISTORY SPTR40_18f 1 170 NSINGLE INITIAL MOTIF SETS RVDCCALPHA11 Length of motif = 15 Motif number = 1 R-type voltage-dependent calcium channel alpha-1 subunit motif I - 1 PCODE ST INT AAEELDLQFPCGTQE CCAE_DISOM 266 266 ILEGFDPPHPCGVQG CCAE_HUMAN 258 258 ILEGFDPPHPCGVQG CCAE_MOUSE 259 259 VLEGFDPPHPCGVQG CCAE_RABIT 258 258 ILEGFDPPHPCGVQG CCAE_RAT 209 209 RVDCCALPHA12 Length of motif = 12 Motif number = 2 R-type voltage-dependent calcium channel alpha-1 subunit motif II - 1 PCODE ST INT CPNGTVCSYWIG CCAE_DISOM 285 4 CPAGYECKDWIG CCAE_HUMAN 273 0 CPAGYECKDWIG CCAE_MOUSE 274 0 CPAGYECKDWIG CCAE_RABIT 273 0 CPAGYECKDWIG CCAE_RAT 224 0 RVDCCALPHA13 Length of motif = 13 Motif number = 3 R-type voltage-dependent calcium channel alpha-1 subunit motif III - 1 PCODE ST INT RRKERMLRISIRH CCAE_DISOM 473 176 RHKERLLRISIRH CCAE_HUMAN 459 174 RHKERLLRISIRH CCAE_MOUSE 460 174 RHKERLLRISVRH CCAE_RABIT 459 174 RHKERLLRISIRH CCAE_RAT 410 174 RVDCCALPHA14 Length of motif = 14 Motif number = 4 R-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1 PCODE ST INT GEQGRALGRSVEAG CCAE_DISOM 866 380 PCHGNCDPTQQEAG CCAE_HUMAN 886 414 SCHGNCDPIQQEAG CCAE_MOUSE 888 415 PCHGNCEPALQETA CCAE_RABIT 878 406 SCHGNCDPTQQETG CCAE_RAT 838 415 RVDCCALPHA15 Length of motif = 11 Motif number = 5 R-type voltage-dependent calcium channel alpha-1 subunit motif V - 1 PCODE ST INT LEESAETSLSR CCAE_DISOM 905 25 GKESSSASRSR CCAE_HUMAN 929 29 GKDSASASRSR CCAE_MOUSE 931 29 AKESSSASRSR CCAE_RABIT 921 29 GKESASASRSR CCAE_RAT 881 29 RVDCCALPHA16 Length of motif = 20 Motif number = 6 R-type voltage-dependent calcium channel alpha-1 subunit motif VI - 1 PCODE ST INT TQEQTEIDVDCENTETPMDS CCAE_DISOM 1036 120 TTESTSVTVAIPDVDPLVDS CCAE_HUMAN 1063 123 TTESTSVTVAIPDVDPLVDS CCAE_MOUSE 1066 124 TTESTDVTVAIPDAEPLVDS CCAE_RABIT 1055 123 TTESTSVTVAIPDVDPLVDS CCAE_RAT 1016 124 FINAL MOTIF SETS RVDCCALPHA11 Length of motif = 15 Motif number = 1 R-type voltage-dependent calcium channel alpha-1 subunit motif I - 1 PCODE ST INT ILEGFDPPHPCGVQG CCAE_RAT 209 209 ILEGFDPPHPCGVQG CCAE_HUMAN 258 258 ILEGFDPPHPCGVQG CCAE_MOUSE 259 259 VLEGFDPPHPCGVQG CCAE_RABIT 258 258 AAEELDLQFPCGTQE CCAE_DISOM 266 266 RVDCCALPHA12 Length of motif = 12 Motif number = 2 R-type voltage-dependent calcium channel alpha-1 subunit motif II - 1 PCODE ST INT CPAGYECKDWIG CCAE_RAT 224 0 CPAGYECKDWIG CCAE_HUMAN 273 0 CPAGYECKDWIG CCAE_MOUSE 274 0 CPAGYECKDWIG CCAE_RABIT 273 0 CPNGTVCSYWIG CCAE_DISOM 285 4 RVDCCALPHA13 Length of motif = 13 Motif number = 3 R-type voltage-dependent calcium channel alpha-1 subunit motif III - 1 PCODE ST INT RHKERLLRISIRH CCAE_RAT 410 174 RHKERLLRISIRH CCAE_HUMAN 459 174 RHKERLLRISIRH CCAE_MOUSE 460 174 RHKERLLRISVRH CCAE_RABIT 459 174 RRKERMLRISIRH CCAE_DISOM 473 176 RVDCCALPHA14 Length of motif = 14 Motif number = 4 R-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1 PCODE ST INT SCHGNCDPTQQETG CCAE_RAT 838 415 PCHGNCDPTQQEAG CCAE_HUMAN 886 414 SCHGNCDPIQQEAG CCAE_MOUSE 888 415 PCHGNCEPALQETA CCAE_RABIT 878 406 GEQGRALGRSVEAG CCAE_DISOM 866 380 RVDCCALPHA15 Length of motif = 11 Motif number = 5 R-type voltage-dependent calcium channel alpha-1 subunit motif V - 1 PCODE ST INT GKESASASRSR CCAE_RAT 881 29 GKESSSASRSR CCAE_HUMAN 929 29 GKDSASASRSR CCAE_MOUSE 931 29 AKESSSASRSR CCAE_RABIT 921 29 LEESAETSLSR CCAE_DISOM 905 25 RVDCCALPHA16 Length of motif = 20 Motif number = 6 R-type voltage-dependent calcium channel alpha-1 subunit motif VI - 1 PCODE ST INT TTESTSVTVAIPDVDPLVDS CCAE_RAT 1016 124 TTESTSVTVAIPDVDPLVDS CCAE_HUMAN 1063 123 TTESTSVTVAIPDVDPLVDS CCAE_MOUSE 1066 124 TTESTDVTVAIPDAEPLVDS CCAE_RABIT 1055 123 TQEQTEIDVDCENTETPMDS CCAE_DISOM 1036 120

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