WORKLIST ENTRIES (1):

LVDCCALPHA1C View alignment     Voltage-dependent L-type calcium channel alpha-1C subunit signature
 Type of fingerprint: COMPOUND with 13 elements
Links:
   PRINTS; PR00167 CACHANNEL; PR01629 TVDCCALPHA1; PR01630 LVDCCALPHA1
   PRINTS; PR01631 NVDCCALPHA1; PR01632 PQVDCCALPHA1; PR01633 RVDCCALPHA1 
   PRINTS; PR01634 LVDCCALPHA1S; PR01636 LVDCCALPHA1D

 Creation date 20-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. TAKIMOTO, K., LI, D., NERBONNE, J.M. AND LEVITAN, E.S.
   Distribution, splicing and glucocorticoid-induced expression of cardiac
   alpha 1C and alpha 1D voltage-gated Ca2+ channel mRNAs.
   J.MOL.CELL CARDIOL. 29(11) 3035-42 (1997).

   6. SOLDATOV, N.M., ZUHLKE, R.D., BOURON, A. AND REUTER, H.
   Molecular structures involved in L-type calcium channel inactivation. Role
   of the carboxyl-terminal region encoded by exons 40-42 in alpha1C subunit in
   the kinetics and Ca2+ dependence of inactivation.
   J.BIOL.CHEM. 272 3560-3566 (1997).

   7. WEI, X., NEELY, A., OLCESE, R., LANG, W., STEFANI, E. AND BIRNBAUMER, L.
   Increase in Ca2+ channel expression by deletions at the amino terminus of
   the cardiac alpha 1C subunit.
   RECEPTORS CHANNELS 4(4) 205-215 (1996).

   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]. L-type calcium channels are
   formed from alpha-1S, alpha-1C and alpha-1D subunits. They are widely 
   distributed and are well characterised in the heart, smooth and skeletal
   muscle, and some neurons. Their primary functions are in both excitation-
   contraction and excitation-secretion coupling. In skeletal muscle, the 
   L-type calcium channels act as a voltage sensor for excitation-contraction
   coupling and, in cardiac muscle, they provide a pathway for calcium influx. 
   Mutations affecting L-type channel subunits result in three diseases: 
   (1) muscular dystrophy, which is characterised by a lack of functional 
   skeletal muscle; (2) hypokalaemic periodic paralysis, which is characterised
   by episodic attacks of skeletal muscle weakness; and (3) malignant
   hyperthermia, which is the main cause of death due to anaesthesia [3].
   
   Alpha1-C subunits can be found in a number of excitable tissues, as well as
   the heart and lungs [5]. The variability in the C-terminal region of the
   alpha-1C subunit generated by alternative splicing influences the kinetics,
   calcium- and voltage-dependence of L-type channels [6]. The N-terminus
   is also a site of significant structural diversity [7].
  
   LVDCCALPHA1C is a 13-element fingerprint that provides a signature for the
   voltage-dependent L-type calcium channel alpha-1C subunit. The fingerprint
   was derived from an initial alignment of 5 sequences: the motifs were drawn 
   from conserved regions spanning the full alignment length, focusing on those
   sections that characterise the alpha-1C subunit but distinguish it from
   other members of the alpha-1 subunit family - motifs 1-3 reside at the 
   N-terminus; motifs 4-6 lie in the cytoplasmic region between TM domain 6 of 
   repeat II and TM domain 1 of repeat III; motif 7 encodes part of repeat IV;
   and motifs 8-13 span the cytoplasmic region between TM domain 6 of repeat IV
   and TM domain 1 of repeat V. 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 13 elements
      0 codes involving 12 elements
      0 codes involving 11 elements
      0 codes involving 10 elements
      0 codes involving  9 elements
      0 codes involving  8 elements
      0 codes involving  7 elements
      0 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
  
   13|   5    5    5    5    5    5    5    5    5    5    5    5    5  
   12|   0    0    0    0    0    0    0    0    0    0    0    0    0  
   11|   0    0    0    0    0    0    0    0    0    0    0    0    0  
   10|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    9|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    8|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    7|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    6|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    5|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    4|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    3|   0    0    0    0    0    0    0    0    0    0    0    0    0  
    2|   0    0    0    0    0    0    0    0    0    0    0    0    0  
   --+------------------------------------------------------------------
     |   1    2    3    4    5    6    7    8    9   10   11   12   13  

True positives..
 CCAC_RAT       CCAC_MOUSE     CCAC_HUMAN     CCAC_RABIT     
 Q9Z305         


  PROTEIN TITLES
   CCAC_RAT         Voltage-dependent L-type calcium channel alpha-1C subunit (C
   CCAC_MOUSE       Voltage-dependent L-type calcium channel alpha-1C subunit (C
   CCAC_HUMAN       Voltage-dependent L-type calcium channel alpha-1C subunit (C
   CCAC_RABIT       Voltage-dependent L-type calcium channel alpha-1C subunit (C
   Q9Z305           L-TYPE CALCIUM CHANNEL ALPHA 1 SUBUNIT - Cavia porcellus (Gu

SCAN HISTORY SPTR40_18f 1 50 NSINGLE INITIAL MOTIF SETS LVDCCALPHA1C1 Length of motif = 16 Motif number = 1 Voltage-dependent L-type calcium channel alpha-1C subunit motif I - 1 PCODE ST INT GSNYGSPRPAHANMNA CCAC_HUMAN 17 17 GSNYGSPRPAHANMNA CCAC_MOUSE 17 17 GSNYGSPRPAHANMNA CCAC_RABIT 47 47 GSNYGSPRPAHANINA Q9Z305 46 46 GSNYGSPRPAHANMNA CCAC_RAT 47 47 LVDCCALPHA1C2 Length of motif = 16 Motif number = 2 Voltage-dependent L-type calcium channel alpha-1C subunit motif II - 1 PCODE ST INT NAAAGLAPEHIPTPGA CCAC_HUMAN 33 0 NAAAGLAPEHIPTPGA CCAC_MOUSE 33 0 NAAAGLAPEHIPTPGA CCAC_RABIT 63 0 NAAAGLAPEHIPTPGA Q9Z305 62 0 NAAAGLAPEHIPTPGA CCAC_RAT 63 0 LVDCCALPHA1C3 Length of motif = 17 Motif number = 3 Voltage-dependent L-type calcium channel alpha-1C subunit motif III - 1 PCODE ST INT LMGSAGNATISTVSSTQ CCAC_HUMAN 64 15 LMGSAGNATISTVSSTQ CCAC_MOUSE 64 15 LMGSAGNATISTVSSTQ CCAC_RABIT 94 15 LMGSAGNTTISTVSSTQ Q9Z305 93 15 LMGSAGNATISTVSSTQ CCAC_RAT 94 15 LVDCCALPHA1C4 Length of motif = 20 Motif number = 4 Voltage-dependent L-type calcium channel alpha-1C subunit motif IV - 1 PCODE ST INT QELVEKPAVGESKEEKIELK CCAC_HUMAN 788 707 QEVMEKPAVEESKEEKIELK CCAC_MOUSE 788 707 QEVVGKPALEEAKEEKIELK CCAC_RABIT 818 707 QEVVEKPAVEETKEEKIELK Q9Z305 817 707 QEVMEKPAVEESKEEKIELK CCAC_RAT 818 707 LVDCCALPHA1C5 Length of motif = 20 Motif number = 5 Voltage-dependent L-type calcium channel alpha-1C subunit motif V - 1 PCODE ST INT SITADGESPPATKINMDDLQ CCAC_HUMAN 808 0 SITADGESPPTTKINMDDLQ CCAC_MOUSE 808 0 SITADGESPPTTKINMDDLQ CCAC_RABIT 838 0 SITADGESPPTTKINMDDLQ Q9Z305 837 0 SITADGESPPTTKINMDDLQ CCAC_RAT 838 0 LVDCCALPHA1C6 Length of motif = 17 Motif number = 6 Voltage-dependent L-type calcium channel alpha-1C subunit motif VI - 1 PCODE ST INT PNENEDKSPYPNPETTG CCAC_HUMAN 828 0 PSENEDKSPHSNPDTAG CCAC_MOUSE 828 0 PNESEDKSPYPNPETTG CCAC_RABIT 858 0 PNENEDKSPYPNPDAAG Q9Z305 857 0 PSENEDKSPHSNPDTAG CCAC_RAT 858 0 LVDCCALPHA1C7 Length of motif = 15 Motif number = 7 Voltage-dependent L-type calcium channel alpha-1C subunit motif VII - 1 PCODE ST INT APESEPSNSTEGETP CCAC_HUMAN 1480 635 APESEPSNSTEGETP CCAC_MOUSE 1432 587 APESEPHNSTEGETP CCAC_RABIT 1462 587 APESDPSNSTEGETP Q9Z305 1461 587 APESEPSNSTEGETP CCAC_RAT 1461 586 LVDCCALPHA1C8 Length of motif = 13 Motif number = 8 Voltage-dependent L-type calcium channel alpha-1C subunit motif VIII - 1 PCODE ST INT LDKAMKEAVSAAS CCAC_HUMAN 1727 232 LDKAMKEAVSAAS CCAC_MOUSE 1679 232 LDKAMKEAVSAAS CCAC_RABIT 1709 232 LDKAMKEAVSAAS Q9Z305 1708 232 LDKAMKEAVSAAS CCAC_RAT 1708 232 LVDCCALPHA1C9 Length of motif = 19 Motif number = 9 Voltage-dependent L-type calcium channel alpha-1C subunit motif IX - 1 PCODE ST INT TESPSHEKLVDSTFTPSSY CCAC_HUMAN 1788 48 TESPSHEKLVDSTFTPSSY CCAC_MOUSE 1740 48 TESPSHEKLVDSTFTPSSY CCAC_RABIT 1770 48 TESPSHEKLVDSTFTPSSY Q9Z305 1769 48 TESPSHEKLVDSTFTPSSY CCAC_RAT 1769 48 LVDCCALPHA1C10 Length of motif = 17 Motif number = 10 Voltage-dependent L-type calcium channel alpha-1C subunit motif X - 1 PCODE ST INT SSTGSNANINNANNTAL CCAC_HUMAN 1807 0 SSTGSNANINNANNTAL CCAC_MOUSE 1759 0 SSTGSNANINNANNTAL CCAC_RABIT 1789 0 SSTGSNANISNANNTAL Q9Z305 1788 0 SSTGSNANINNANNTAL CCAC_RAT 1788 0 LVDCCALPHA1C11 Length of motif = 21 Motif number = 11 Voltage-dependent L-type calcium channel alpha-1C subunit motif XI - 1 PCODE ST INT EACSEPSLLSTEMLSYQDDEN CCAC_HUMAN 1929 105 EYCSEPSLLSTDMFSYQEDEH CCAC_MOUSE 1845 69 ECCSEPSLLSTEMLSYQDDEN CCAC_RABIT 1876 70 EYCSEPSLLSTEMLSYKDDEN Q9Z305 1875 70 EYCSEPSLLSTDILSYQDDEN CCAC_RAT 1875 70 LVDCCALPHA1C12 Length of motif = 11 Motif number = 12 Voltage-dependent L-type calcium channel alpha-1C subunit motif XII - 1 PCODE ST INT GGDISQKTVLP CCAC_HUMAN 1994 44 GGDISQKTALP CCAC_MOUSE 1910 44 GGDISQKTVLP CCAC_RABIT 1941 44 GGDISQKTVLP Q9Z305 1940 44 GGDISQKTALP CCAC_RAT 1940 44 LVDCCALPHA1C13 Length of motif = 15 Motif number = 13 Voltage-dependent L-type calcium channel alpha-1C subunit motif XIII - 1 PCODE ST INT PVPTLRLEGVESSEK CCAC_HUMAN 2051 46 PIPTLRLEGAESSEK CCAC_MOUSE 1967 46 PIPTLRLEGADSSEK CCAC_RABIT 1998 46 PIPTLRLEGAESCEK Q9Z305 1997 46 PIPTLRLEGAESSEK CCAC_RAT 1997 46 FINAL MOTIF SETS LVDCCALPHA1C1 Length of motif = 16 Motif number = 1 Voltage-dependent L-type calcium channel alpha-1C subunit motif I - 1 PCODE ST INT GSNYGSPRPAHANMNA CCAC_RAT 47 47 GSNYGSPRPAHANMNA CCAC_MOUSE 17 17 GSNYGSPRPAHANMNA CCAC_HUMAN 17 17 GSNYGSPRPAHANMNA CCAC_RABIT 47 47 GSNYGSPRPAHANINA Q9Z305 46 46 LVDCCALPHA1C2 Length of motif = 16 Motif number = 2 Voltage-dependent L-type calcium channel alpha-1C subunit motif II - 1 PCODE ST INT NAAAGLAPEHIPTPGA CCAC_RAT 63 0 NAAAGLAPEHIPTPGA CCAC_MOUSE 33 0 NAAAGLAPEHIPTPGA CCAC_HUMAN 33 0 NAAAGLAPEHIPTPGA CCAC_RABIT 63 0 NAAAGLAPEHIPTPGA Q9Z305 62 0 LVDCCALPHA1C3 Length of motif = 17 Motif number = 3 Voltage-dependent L-type calcium channel alpha-1C subunit motif III - 1 PCODE ST INT LMGSAGNATISTVSSTQ CCAC_RAT 94 15 LMGSAGNATISTVSSTQ CCAC_MOUSE 64 15 LMGSAGNATISTVSSTQ CCAC_HUMAN 64 15 LMGSAGNATISTVSSTQ CCAC_RABIT 94 15 LMGSAGNTTISTVSSTQ Q9Z305 93 15 LVDCCALPHA1C4 Length of motif = 20 Motif number = 4 Voltage-dependent L-type calcium channel alpha-1C subunit motif IV - 1 PCODE ST INT QEVMEKPAVEESKEEKIELK CCAC_RAT 818 707 QEVMEKPAVEESKEEKIELK CCAC_MOUSE 788 707 QELVEKPAVGESKEEKIELK CCAC_HUMAN 788 707 QEVVGKPALEEAKEEKIELK CCAC_RABIT 818 707 QEVVEKPAVEETKEEKIELK Q9Z305 817 707 LVDCCALPHA1C5 Length of motif = 20 Motif number = 5 Voltage-dependent L-type calcium channel alpha-1C subunit motif V - 1 PCODE ST INT SITADGESPPTTKINMDDLQ CCAC_RAT 838 0 SITADGESPPTTKINMDDLQ CCAC_MOUSE 808 0 SITADGESPPATKINMDDLQ CCAC_HUMAN 808 0 SITADGESPPTTKINMDDLQ CCAC_RABIT 838 0 SITADGESPPTTKINMDDLQ Q9Z305 837 0 LVDCCALPHA1C6 Length of motif = 17 Motif number = 6 Voltage-dependent L-type calcium channel alpha-1C subunit motif VI - 1 PCODE ST INT PSENEDKSPHSNPDTAG CCAC_RAT 858 0 PSENEDKSPHSNPDTAG CCAC_MOUSE 828 0 PNENEDKSPYPNPETTG CCAC_HUMAN 828 0 PNESEDKSPYPNPETTG CCAC_RABIT 858 0 PNENEDKSPYPNPDAAG Q9Z305 857 0 LVDCCALPHA1C7 Length of motif = 15 Motif number = 7 Voltage-dependent L-type calcium channel alpha-1C subunit motif VII - 1 PCODE ST INT APESEPSNSTEGETP CCAC_RAT 1461 586 APESEPSNSTEGETP CCAC_MOUSE 1432 587 APESEPSNSTEGETP CCAC_HUMAN 1480 635 APESEPHNSTEGETP CCAC_RABIT 1462 587 APESDPSNSTEGETP Q9Z305 1461 587 LVDCCALPHA1C8 Length of motif = 13 Motif number = 8 Voltage-dependent L-type calcium channel alpha-1C subunit motif VIII - 1 PCODE ST INT LDKAMKEAVSAAS CCAC_RAT 1708 232 LDKAMKEAVSAAS CCAC_MOUSE 1679 232 LDKAMKEAVSAAS CCAC_HUMAN 1727 232 LDKAMKEAVSAAS CCAC_RABIT 1709 232 LDKAMKEAVSAAS Q9Z305 1708 232 LVDCCALPHA1C9 Length of motif = 19 Motif number = 9 Voltage-dependent L-type calcium channel alpha-1C subunit motif IX - 1 PCODE ST INT TESPSHEKLVDSTFTPSSY CCAC_RAT 1769 48 TESPSHEKLVDSTFTPSSY CCAC_MOUSE 1740 48 TESPSHEKLVDSTFTPSSY CCAC_HUMAN 1788 48 TESPSHEKLVDSTFTPSSY CCAC_RABIT 1770 48 TESPSHEKLVDSTFTPSSY Q9Z305 1769 48 LVDCCALPHA1C10 Length of motif = 17 Motif number = 10 Voltage-dependent L-type calcium channel alpha-1C subunit motif X - 1 PCODE ST INT SSTGSNANINNANNTAL CCAC_RAT 1788 0 SSTGSNANINNANNTAL CCAC_MOUSE 1759 0 SSTGSNANINNANNTAL CCAC_HUMAN 1807 0 SSTGSNANINNANNTAL CCAC_RABIT 1789 0 SSTGSNANISNANNTAL Q9Z305 1788 0 LVDCCALPHA1C11 Length of motif = 21 Motif number = 11 Voltage-dependent L-type calcium channel alpha-1C subunit motif XI - 1 PCODE ST INT EYCSEPSLLSTDILSYQDDEN CCAC_RAT 1875 70 EYCSEPSLLSTDMFSYQEDEH CCAC_MOUSE 1845 69 EACSEPSLLSTEMLSYQDDEN CCAC_HUMAN 1929 105 ECCSEPSLLSTEMLSYQDDEN CCAC_RABIT 1876 70 EYCSEPSLLSTEMLSYKDDEN Q9Z305 1875 70 LVDCCALPHA1C12 Length of motif = 11 Motif number = 12 Voltage-dependent L-type calcium channel alpha-1C subunit motif XII - 1 PCODE ST INT GGDISQKTALP CCAC_RAT 1940 44 GGDISQKTALP CCAC_MOUSE 1910 44 GGDISQKTVLP CCAC_HUMAN 1994 44 GGDISQKTVLP CCAC_RABIT 1941 44 GGDISQKTVLP Q9Z305 1940 44 LVDCCALPHA1C13 Length of motif = 15 Motif number = 13 Voltage-dependent L-type calcium channel alpha-1C subunit motif XIII - 1 PCODE ST INT PIPTLRLEGAESSEK CCAC_RAT 1997 46 PIPTLRLEGAESSEK CCAC_MOUSE 1967 46 PVPTLRLEGVESSEK CCAC_HUMAN 2051 46 PIPTLRLEGADSSEK CCAC_RABIT 1998 46 PIPTLRLEGAESCEK Q9Z305 1997 46

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