SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR01630

Identifier
LVDCCALPHA1  [View Relations]  [View Alignment]  
Accession
PR01630
No. of Motifs
6
Creation Date
11-DEC-2001
Title
L-type voltage-dependent calcium channel alpha-1 subunit signature
Database References
PRINTS; PR00167 CACHANNEL; PR01635 LVDCCALPHA1C; PR01636 LVDCCALPHA1D
PRINTS; PR01634 LVDCCALPHA1S
Literature References
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).

Documentation
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].
 
LVDCCALPHA1 is a 6-element fingerprint that provides a signature for the
L-type voltage-dependent calcium channel alpha-1 subunit. The fingerprint
was derived from an initial alignment of 13 sequences: the motifs were drawn
from conserved regions spanning the full alignment length: motif 1 lies in
the extracellular region between TM domains 1 and 2 of repeat I; motif 2
resides in TM domain 3 of repeat I; motif 3 encodes the cytoplasmic region
between TM domain 6 of repeat I and TM domain 1 of repeat II; motif 4 lies
in the cytoplasmic region of repeat II; motif 5 spans TM domain 3 of repeat 
II; and motif 6 resides in the extracellular region between TM domains
5 and 6 in repeat II. Two iterations on SPTR40_18f were required to reach
convergence, at which point a true set comprising 18 sequences was
identified. Several partial matches were also found, all of which are
members of the L-type voltage-dependent calcium channel family that fail 
to make significant matches with one or more motifs.
Summary Information
  18 codes involving  6 elements
1 codes involving 5 elements
0 codes involving 4 elements
6 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
6181818181818
5111110
4000000
3605061
2100010
123456
True Positives
CCAD_MESAU    CIC1_CYPCA    CIC1_RABIT    CICB_RAT      
CICC_RABIT CICC_RAT O57483 O60840
O73700 O95226 Q01668 Q01815
Q02789 Q13698 Q13936 Q9JIS7
Q9UHB1 Q9Z305
True Positive Partials
Codes involving 5 elements
O96057
Codes involving 3 elements
O17050 O97017 Q18698 Q24270
Q25452 Q9V3P7
Codes involving 2 elements
O02038
Sequence Titles
CCAD_MESAU  Voltage-dependent L-type calcium channel alpha-1D subunit (Calcium channel, L type, alpha-1 polypeptide isoform 2) - Mesocricetus auratus (Golden hamster). 
CIC1_CYPCA DIHYDROPYRIDINE-SENSITIVE L-TYPE, SKELETAL MUSCLE CALCIUM CHANNEL ALPHA-1 SUBUNIT - CYPRINUS CARPIO (COMMON CARP).
CIC1_RABIT DIHYDROPYRIDINE-SENSITIVE L-TYPE, SKELETAL MUSCLE CALCIUM CHANNEL ALPHA-1 SUBUNIT - ORYCTOLAGUS CUNICULUS (RABBIT).
CICB_RAT VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1D SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 2) (RAT BRAIN CLASS D) (RBD) - RATTUS NORVEGICUS (RAT).
CICC_RABIT VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 1, CARDIAC MUSCLE) (SMOOTH MUSCLE CALCIUM CHANNEL BLOCKER RECEPTOR) (CACB-RECEPTOR) - ORYCTOLAGUS CUNICULUS (RABBIT).
CICC_RAT VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL, ALPHA-1C SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 1, CARDIAC MUSCLE) (RAT BRAIN CLASS C) (RBC) - RATTUS NORVEGICUS (RAT).
O57483 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL, ALPHA-1S SUBUNIT (FGALPHA1S) - Rana catesbeiana (Bull frog).
O60840 L-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT - HOMO SAPIENS (HUMAN).
O73700 L-TYPE VOLTAGE-GATED CALCIUM CHANNEL ALPHA1D SUBUNIT CHCACHA1D - GALLUS GALLUS (CHICKEN).
O95226 VOLTAGE-GATED L-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT - Homo sapiens (Human).
Q01668 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1D SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 2) - HOMO SAPIENS (HUMAN).
Q01815 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL, ALPHA-1C SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 1, CARDIAC MUSCLE) (MOUSE BRAIN CLASS C) (MBC) (MELC-CC) - MUS MUSCULUS (MOUSE).
Q02789 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL, ALPHA-1S SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 3, SKELETAL MUSCLE) - Mus musculus (Mouse).
Q13698 DIHYDROPRYRIDINE-SENSITIVE L-TYPE, SKELETAL MUSCLE CALCIUM CHANNEL ALPHA-1 SUBUNIT - HOMO SAPIENS (HUMAN).
Q13936 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 1, CARDIAC MUSCLE) - HOMO SAPIENS (HUMAN).
Q9JIS7 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1F SUBUNIT - Mus musculus (Mouse).
Q9UHB1 VOLTAGE-GATED L-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT - Homo sapiens (Human).
Q9Z305 L-TYPE CALCIUM CHANNEL ALPHA 1 SUBUNIT - Cavia porcellus (Guinea pig).

O96057 ASCIDIAN CALCIUM CHANNEL ALPHA1-SUBUNIT - Halocynthia roretzi (Sea squirt).

O17050 PUTATIVE L-TYPE CALCIUM CHANNEL ALPHA 1 SUBUNIT - Caenorhabditis elegans.
O97017 L-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT - Stylophora pistillata.
Q18698 HYPOTHETICAL PROTEIN C48A7.1 - Caenorhabditis elegans.
Q24270 CALCIUM CHANNEL ALPHA-1 SUBUNIT - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q25452 VOLTAGE DEPENDENT CALCIUM CHANNEL ALPHA1 SUBUNIT - MUSCA DOMESTICA (HOUSE FLY).
Q9V3P7 CA-ALPHA1D PROTEIN - Drosophila melanogaster (Fruit fly).

O02038 VOLTAGE-GATED CALCIUM CHANNEL ALPHA-1 SUBUNIT - Cyanea capillata (Lion's mane jellyfish).
Scan History
SPTR40_18f 2  150  NSINGLE    
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
SNATNSNLERVEYLFLIIF Q13936 152 152 -
SNATNSNLERVEYLFLIIF Q01815 152 152 -
SNATNSNLERVEYLFLIIF CICC_RABIT 182 182 -
SNSTNHNLEKVEYAFLIIF Q01668 154 154 -
SNSTNHNLEKVEYAFLIIF CICB_RAT 154 154 -
SNSTNHNLEKVEYAFLIIF CCAD_MESAU 153 153 -
SNATNSNLERVEYLFLIIF Q9Z305 181 181 -
SNTANHNLEQVEYVFLVIF O60840 120 120 -
SNTANHNLEQVEYVFLVIF O95226 55 55 -
NNSLNLGLEKLEYFFLIVF Q13698 79 79 -
NNSLNLGLEKLEYFFLTVF CIC1_RABIT 79 79 -
TNNTNLTLESLEYIFLVIF CIC1_CYPCA 98 98 -

Motif 2 width=12
Element Seqn Id St Int Rpt
VVVGLFSAILEQ Q13936 203 32 -
VVVGLFSAILEQ Q01815 203 32 -
VVVGLFSAILEQ CICC_RABIT 233 32 -
VIVGLFSVILEQ Q01668 205 32 -
VIVGLFSVILEQ CICB_RAT 205 32 -
VIVGLFSVILEQ CCAD_MESAU 204 32 -
VVVGLFSAILEQ Q9Z305 232 32 -
VVVGLFSVLLEQ O60840 171 32 -
VVVGLFSVLLEQ O95226 106 32 -
VFLGVFTVILEQ Q13698 130 32 -
VFLGVFTAILEQ CIC1_RABIT 130 32 -
VFMGLFTLVVDT CIC1_CYPCA 149 32 -

Motif 3 width=14
Element Seqn Id St Int Rpt
KAKARGDFQKLREK Q13936 414 199 -
KAKARGDFQKLREK Q01815 414 199 -
KAKARGDFQKLREK CICC_RABIT 444 199 -
KAKARGDFQKLREK Q01668 415 198 -
KAKARGDFQKLREK CICB_RAT 415 198 -
KAKARGDFQKLREN CCAD_MESAU 414 198 -
KAKARGDFQKLREK Q9Z305 443 199 -
KAKARGDFQKQREK O60840 381 198 -
KAKARGDFQKQREK O95226 316 198 -
KAKSRGTFQKLREK Q13698 343 201 -
KAKSRGTFQKLREK CIC1_RABIT 343 201 -
ESRSRGEYQKLRER CIC1_CYPCA 360 199 -

Motif 4 width=19
Element Seqn Id St Int Rpt
KFSRYWRRWNRFCRRKCRA Q13936 501 73 -
KFSRYWRRWNRFCRRKCRA Q01815 501 73 -
KFSRYWRRWNRFCRRKCRA CICC_RABIT 531 73 -
KLSRRWRRWNRFNRRRCRA Q01668 500 71 -
PYSRRWRRWNRFNRRRCRA CICB_RAT 559 130 -
KLSRRWRRWNRFNRRRCRA CCAD_MESAU 499 71 -
KFSRYWRRWNRFCRRKCRA Q9Z305 530 73 -
RVCRRLRRANRVLRARCRR O60840 495 100 -
RVCRRLRRANRVLRARCRR O95226 441 111 -
QFIRHWRQWNRIFRWKCHD Q13698 409 52 -
QFIRHWRQWNRVFRWKCHD CIC1_RABIT 409 52 -
YFYRLARRWNVVLRRKCHV CIC1_CYPCA 424 50 -

Motif 5 width=16
Element Seqn Id St Int Rpt
RFDCFVVCGGILETIL Q13936 590 70 -
RFDCFIVCGGILETIL Q01815 590 70 -
RFDCFIVCGGILETIL CICC_RABIT 620 70 -
RFDCFVVCGGITETIL Q01668 589 70 -
RFDCFVVCGGITETIL CICB_RAT 648 70 -
RFDCFVVCGGITETIL CCAD_MESAU 588 70 -
RLDCFIVCGGILETIL Q9Z305 619 70 -
RFDCFVVCGGILETTL O60840 584 70 -
RFDCFVVCGGILETTL O95226 530 70 -
RFDCFVVCSGILEILL Q13698 498 70 -
RFDCFVVCSGILELLL CIC1_RABIT 498 70 -
RFDCFVVTIGILEIIL CIC1_CYPCA 513 70 -

Motif 6 width=14
Element Seqn Id St Int Rpt
NFDEMQTRRSTFDN Q13936 678 72 -
NFDEMQTRRSTFDN Q01815 678 72 -
NFDEMQTRRSTFDN CICC_RABIT 708 72 -
NFDETQTKRSTFDN Q01668 677 72 -
NFDETQTKRSTFDN CICB_RAT 736 72 -
NFDETQTKRSTFDN CCAD_MESAU 676 72 -
NFDEMRTRRSTFDN Q9Z305 707 72 -
NFDQTHTKRSTFDT O60840 672 72 -
NFDQTHTKRSTFDT O95226 618 72 -
DFEDTEVRRSNFDN Q13698 586 72 -
DFEDTEVRRSNFDN CIC1_RABIT 586 72 -
NFPDRVIQRSNFDN CIC1_CYPCA 601 72 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
SNSTNHNLEKVEYAFLIIF O73700 149 149 -
SNATNSNLERVEYLFLIIF Q13936 152 152 -
SNATNSNLERVEYLFLIIF Q01815 152 152 -
SNATNSNLERVEYLFLIIF CICC_RABIT 182 182 -
SNATNSNLERVEYLFLIIF CICC_RAT 182 182 -
SNSTNHNLEKVEYAFLIIF Q01668 154 154 -
SNSTNHNLEKVEYAFLIIF CICB_RAT 154 154 -
SNSTNHNLEKVEYAFLIIF CCAD_MESAU 153 153 -
SNATNSNLERVEYLFLIIF Q9Z305 181 181 -
SNTANHNLEQVEYVFLVIF Q9JIS7 120 120 -
SNTANHNLEQVEYVFLVIF O60840 120 120 -
SNTANHNLEQVEYVFLVIF O95226 55 55 -
SNTANHNLEQVEYVFLVIF Q9UHB1 120 120 -
NNTLNLGLEKLEYFFLIVF Q02789 79 79 -
NNSLNLGLEKLEYFFLIVF Q13698 79 79 -
NNSLNLGLEKLEYFFLTVF CIC1_RABIT 79 79 -
TNSTNSVLEKVEYIFLFIF O57483 79 79 -
TNNTNLTLESLEYIFLVIF CIC1_CYPCA 98 98 -

Motif 2 width=12
Element Seqn Id St Int Rpt
VVVGLFSVILEQ O73700 200 32 -
VVVGLFSAILEQ Q13936 203 32 -
VVVGLFSAILEQ Q01815 203 32 -
VVVGLFSAILEQ CICC_RABIT 233 32 -
VVVGLFSAILEQ CICC_RAT 233 32 -
VIVGLFSVILEQ Q01668 205 32 -
VIVGLFSVILEQ CICB_RAT 205 32 -
VIVGLFSVILEQ CCAD_MESAU 204 32 -
VVVGLFSAILEQ Q9Z305 232 32 -
VVVGLFSVLLEQ Q9JIS7 171 32 -
VVVGLFSVLLEQ O60840 171 32 -
VVVGLFSVLLEQ O95226 106 32 -
VVVGLFSVLLEQ Q9UHB1 171 32 -
VFLGVFTVILEQ Q02789 130 32 -
VFLGVFTVILEQ Q13698 130 32 -
VFLGVFTAILEQ CIC1_RABIT 130 32 -
VSVGVFSVLLEQ O57483 130 32 -
VFMGLFTLVVDT CIC1_CYPCA 149 32 -

Motif 3 width=14
Element Seqn Id St Int Rpt
KAKARGDFQKLREK O73700 410 198 -
KAKARGDFQKLREK Q13936 414 199 -
KAKARGDFQKLREK Q01815 414 199 -
KAKARGDFQKLREK CICC_RABIT 444 199 -
KAKARGDFQKLREK CICC_RAT 444 199 -
KAKARGDFQKLREK Q01668 415 198 -
KAKARGDFQKLREK CICB_RAT 415 198 -
KAKARGDFQKLREN CCAD_MESAU 414 198 -
KAKARGDFQKLREK Q9Z305 443 199 -
KAKARGDFQKLREK Q9JIS7 381 198 -
KAKARGDFQKQREK O60840 381 198 -
KAKARGDFQKQREK O95226 316 198 -
KAKARGDFQKQREK Q9UHB1 381 198 -
KAKSRGTFQKLREK Q02789 343 201 -
KAKSRGTFQKLREK Q13698 343 201 -
KAKSRGTFQKLREK CIC1_RABIT 343 201 -
KAKSRGAFQMLREQ O57483 341 199 -
ESRSRGEYQKLRER CIC1_CYPCA 360 199 -

Motif 4 width=19
Element Seqn Id St Int Rpt
KFSRRWRRWNRFNRRKCRA O73700 521 97 -
KFSRYWRRWNRFCRRKCRA Q13936 501 73 -
KFSRYWRRWNRFCRRKCRA Q01815 501 73 -
KFSRYWRRWNRFCRRKCRA CICC_RABIT 531 73 -
KFSRYWRRWNRFCRRKCRA CICC_RAT 531 73 -
KLSRRWRRWNRFNRRRCRA Q01668 500 71 -
PYSRRWRRWNRFNRRRCRA CICB_RAT 559 130 -
KLSRRWRRWNRFNRRRCRA CCAD_MESAU 499 71 -
KFSRYWRRWNRFCRRKCRA Q9Z305 530 73 -
RICRHFRRANRGLRARCRR Q9JIS7 506 111 -
RVCRRLRRANRVLRARCRR O60840 495 100 -
RVCRRLRRANRVLRARCRR O95226 441 111 -
RVCRRLRRANRVLRARCRR Q9UHB1 506 111 -
QFIRHWRQWNRVFRWKCHD Q02789 409 52 -
QFIRHWRQWNRIFRWKCHD Q13698 409 52 -
QFIRHWRQWNRVFRWKCHD CIC1_RABIT 409 52 -
AFFRQWRLWHRLLRRKSRD O57483 408 53 -
YFYRLARRWNVVLRRKCHV CIC1_CYPCA 424 50 -

Motif 5 width=16
Element Seqn Id St Int Rpt
RFDCFVVCGGIVETIL O73700 610 70 -
RFDCFVVCGGILETIL Q13936 590 70 -
RFDCFIVCGGILETIL Q01815 590 70 -
RFDCFIVCGGILETIL CICC_RABIT 620 70 -
RFDCFIVCGGILETIL CICC_RAT 620 70 -
RFDCFVVCGGITETIL Q01668 589 70 -
RFDCFVVCGGITETIL CICB_RAT 648 70 -
RFDCFVVCGGITETIL CCAD_MESAU 588 70 -
RLDCFIVCGGILETIL Q9Z305 619 70 -
RFDCFVVCGGILETTL Q9JIS7 595 70 -
RFDCFVVCGGILETTL O60840 584 70 -
RFDCFVVCGGILETTL O95226 530 70 -
RFDCFVVCGGILETTL Q9UHB1 595 70 -
RFDCFVVCSGILEILL Q02789 498 70 -
RFDCFVVCSGILEILL Q13698 498 70 -
RFDCFVVCSGILELLL CIC1_RABIT 498 70 -
RFDSFVVCTGLLEVML O57483 497 70 -
RFDCFVVTIGILEIIL CIC1_CYPCA 513 70 -

Motif 6 width=14
Element Seqn Id St Int Rpt
NFDETQTKRSTFDN O73700 698 72 -
NFDEMQTRRSTFDN Q13936 678 72 -
NFDEMQTRRSTFDN Q01815 678 72 -
NFDEMQTRRSTFDN CICC_RABIT 708 72 -
NFDEMQTRRSTFDN CICC_RAT 708 72 -
NFDETQTKRSTFDN Q01668 677 72 -
NFDETQTKRSTFDN CICB_RAT 736 72 -
NFDETQTKRSTFDN CCAD_MESAU 676 72 -
NFDEMRTRRSTFDN Q9Z305 707 72 -
NFDQTHTKRSTFDT Q9JIS7 683 72 -
NFDQTHTKRSTFDT O60840 672 72 -
NFDQTHTKRSTFDT O95226 618 72 -
NFDQTHTKRSTFDT Q9UHB1 683 72 -
DFEDTEVRRSNFDN Q02789 586 72 -
DFEDTEVRRSNFDN Q13698 586 72 -
DFEDTEVRRSNFDN CIC1_RABIT 586 72 -
DFEDLEVRRSTFDT O57483 585 72 -
NFPDRVIQRSNFDN CIC1_CYPCA 601 72 -