WORKLIST ENTRIES (1):
LVDCCALPHA1 View alignment L-type voltage-dependent calcium channel alpha-1 subunit signature
Type of fingerprint: COMPOUND with 6 elements
Links:
PRINTS; PR00167 CACHANNEL; PR01629 TVDCCALPHA1; PR01631 NVDCCALPHA1
PRINTS; PR01632 PQVDCCALPHA1; PR01633 RVDCCALPHA1
PRINTS; PR01634 LVDCCALPHA1S; PR01635 LVDCCALPHA1C; PR01636 LVDCCALPHA1D
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).
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 FINGERPRINT INDEX
6| 18 18 18 18 18 18
5| 1 1 1 1 1 0
4| 0 0 0 0 0 0
3| 6 0 5 0 6 1
2| 1 0 0 0 1 0
--+-------------------------------
| 1 2 3 4 5 6
True positives..
CCAD_CHICK CCAC_HUMAN CCAC_RAT CCAC_RABIT
CCAC_MOUSE CCAD_HUMAN CCAD_RAT CCAD_MESAU
Q9Z305 Q9JIS7 Q9UHB1 O95226
CCAF_HUMAN Q02789 CCAS_HUMAN CCAS_RABIT
O57483 CCAS_CYPCA
Subfamily: Codes involving 5 elements
Subfamily True positives..
O96057
Subfamily: Codes involving 3 elements
Subfamily True positives..
CCAD_DROME Q9V3P7 CCAM_MUSDO O17050
Q18698 O97017
Subfamily: Codes involving 2 elements
Subfamily True positives..
O02038
PROTEIN TITLES
CCAD_CHICK Voltage-dependent L-type calcium channel alpha-1D subunit (C
CCAC_HUMAN Voltage-dependent L-type calcium channel alpha-1C subunit (C
CCAC_RAT Voltage-dependent L-type calcium channel alpha-1C subunit (C
CCAC_RABIT Voltage-dependent L-type calcium channel alpha-1C subunit (C
CCAC_MOUSE Voltage-dependent L-type calcium channel alpha-1C subunit (C
CCAD_HUMAN Voltage-dependent L-type calcium channel alpha-1D subunit (C
CCAD_RAT Voltage-dependent L-type calcium channel alpha-1D subunit (C
CCAD_MESAU Voltage-dependent L-type calcium channel alpha-1D subunit (C
Q9Z305 L-TYPE CALCIUM CHANNEL ALPHA 1 SUBUNIT - Cavia porcellus (Gu
Q9JIS7 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1F SUBUNIT -
Q9UHB1 VOLTAGE-GATED L-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT - Homo
O95226 VOLTAGE-GATED L-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT - Homo
CCAF_HUMAN Voltage-dependent L-type calcium channel alpha-1F subunit -
Q02789 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL, ALPHA-1S SUBUNIT (
CCAS_HUMAN Voltage-dependent L-type calcium channel alpha-1S subunit (C
CCAS_RABIT Voltage-dependent L-type calcium channel alpha-1S subunit (C
O57483 VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL, ALPHA-1S SUBUNIT (
CCAS_CYPCA Dihydropyridine-sensitive L-type, skeletal muscle calcium ch
O96057 ASCIDIAN CALCIUM CHANNEL ALPHA1-SUBUNIT - Halocynthia roretz
CCAD_DROME Voltage-dependent calcium channel type D alpha-1 subunit (DM
Q9V3P7 CA-ALPHA1D PROTEIN - Drosophila melanogaster (Fruit fly).
CCAM_MUSDO Muscle calcium channel alpha-1 subunit (MDL-alpha1) - Musca
O17050 PUTATIVE L-TYPE CALCIUM CHANNEL ALPHA 1 SUBUNIT - Caenorhabd
Q18698 HYPOTHETICAL PROTEIN C48A7.1 - Caenorhabditis elegans.
O97017 L-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT - Stylophora pistilla
O02038 VOLTAGE-GATED CALCIUM CHANNEL ALPHA-1 SUBUNIT - Cyanea capil
SCAN HISTORY
SPTR40_18f 2 150 NSINGLE
INITIAL MOTIF SETS
LVDCCALPHA11 Length of motif = 19 Motif number = 1
L-type voltage-dependent calcium channel alpha-1 subunit motif I - 1
PCODE ST INT
SNATNSNLERVEYLFLIIF CCAC_HUMAN 152 152
SNATNSNLERVEYLFLIIF CCAC_MOUSE 152 152
SNATNSNLERVEYLFLIIF CCAC_RABIT 182 182
SNSTNHNLEKVEYAFLIIF CCAD_HUMAN 154 154
SNSTNHNLEKVEYAFLIIF CCAD_MESAU 153 153
SNSTNHNLEKVEYAFLIIF CCAD_RAT 154 154
SNTANHNLEQVEYVFLVIF CCAF_HUMAN 120 120
TNNTNLTLESLEYIFLVIF CCAS_CYPCA 98 98
NNSLNLGLEKLEYFFLTVF CCAS_RABIT 79 79
NNSLNLGLEKLEYFFLIVF CCAS_HUMAN 79 79
SNTANHNLEQVEYVFLVIF O95226 55 55
SNATNSNLERVEYLFLIIF Q9Z305 181 181
LVDCCALPHA12 Length of motif = 12 Motif number = 2
L-type voltage-dependent calcium channel alpha-1 subunit motif II - 1
PCODE ST INT
VVVGLFSAILEQ CCAC_HUMAN 203 32
VVVGLFSAILEQ CCAC_MOUSE 203 32
VVVGLFSAILEQ CCAC_RABIT 233 32
VIVGLFSVILEQ CCAD_HUMAN 205 32
VIVGLFSVILEQ CCAD_MESAU 204 32
VIVGLFSVILEQ CCAD_RAT 205 32
VVVGLFSVLLEQ CCAF_HUMAN 171 32
VFMGLFTLVVDT CCAS_CYPCA 149 32
VFLGVFTAILEQ CCAS_RABIT 130 32
VFLGVFTVILEQ CCAS_HUMAN 130 32
VVVGLFSVLLEQ O95226 106 32
VVVGLFSAILEQ Q9Z305 232 32
LVDCCALPHA13 Length of motif = 14 Motif number = 3
L-type voltage-dependent calcium channel alpha-1 subunit motif III - 1
PCODE ST INT
KAKARGDFQKLREK CCAC_HUMAN 414 199
KAKARGDFQKLREK CCAC_MOUSE 414 199
KAKARGDFQKLREK CCAC_RABIT 444 199
KAKARGDFQKLREK CCAD_HUMAN 415 198
KAKARGDFQKLREN CCAD_MESAU 414 198
KAKARGDFQKLREK CCAD_RAT 415 198
KAKARGDFQKQREK CCAF_HUMAN 381 198
ESRSRGEYQKLRER CCAS_CYPCA 360 199
KAKSRGTFQKLREK CCAS_RABIT 343 201
KAKSRGTFQKLREK CCAS_HUMAN 343 201
KAKARGDFQKQREK O95226 316 198
KAKARGDFQKLREK Q9Z305 443 199
LVDCCALPHA14 Length of motif = 19 Motif number = 4
L-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1
PCODE ST INT
KFSRYWRRWNRFCRRKCRA CCAC_HUMAN 501 73
KFSRYWRRWNRFCRRKCRA CCAC_MOUSE 501 73
KFSRYWRRWNRFCRRKCRA CCAC_RABIT 531 73
KLSRRWRRWNRFNRRRCRA CCAD_HUMAN 500 71
KLSRRWRRWNRFNRRRCRA CCAD_MESAU 499 71
PYSRRWRRWNRFNRRRCRA CCAD_RAT 559 130
RVCRRLRRANRVLRARCRR CCAF_HUMAN 495 100
YFYRLARRWNVVLRRKCHV CCAS_CYPCA 424 50
QFIRHWRQWNRVFRWKCHD CCAS_RABIT 409 52
QFIRHWRQWNRIFRWKCHD CCAS_HUMAN 409 52
RVCRRLRRANRVLRARCRR O95226 441 111
KFSRYWRRWNRFCRRKCRA Q9Z305 530 73
LVDCCALPHA15 Length of motif = 16 Motif number = 5
L-type voltage-dependent calcium channel alpha-1 subunit motif V - 1
PCODE ST INT
RFDCFVVCGGILETIL CCAC_HUMAN 590 70
RFDCFIVCGGILETIL CCAC_MOUSE 590 70
RFDCFIVCGGILETIL CCAC_RABIT 620 70
RFDCFVVCGGITETIL CCAD_HUMAN 589 70
RFDCFVVCGGITETIL CCAD_MESAU 588 70
RFDCFVVCGGITETIL CCAD_RAT 648 70
RFDCFVVCGGILETTL CCAF_HUMAN 584 70
RFDCFVVTIGILEIIL CCAS_CYPCA 513 70
RFDCFVVCSGILELLL CCAS_RABIT 498 70
RFDCFVVCSGILEILL CCAS_HUMAN 498 70
RFDCFVVCGGILETTL O95226 530 70
RLDCFIVCGGILETIL Q9Z305 619 70
LVDCCALPHA16 Length of motif = 14 Motif number = 6
L-type voltage-dependent calcium channel alpha-1 subunit motif VI - 1
PCODE ST INT
NFDEMQTRRSTFDN CCAC_HUMAN 678 72
NFDEMQTRRSTFDN CCAC_MOUSE 678 72
NFDEMQTRRSTFDN CCAC_RABIT 708 72
NFDETQTKRSTFDN CCAD_HUMAN 677 72
NFDETQTKRSTFDN CCAD_MESAU 676 72
NFDETQTKRSTFDN CCAD_RAT 736 72
NFDQTHTKRSTFDT CCAF_HUMAN 672 72
NFPDRVIQRSNFDN CCAS_CYPCA 601 72
DFEDTEVRRSNFDN CCAS_RABIT 586 72
DFEDTEVRRSNFDN CCAS_HUMAN 586 72
NFDQTHTKRSTFDT O95226 618 72
NFDEMRTRRSTFDN Q9Z305 707 72
FINAL MOTIF SETS
LVDCCALPHA11 Length of motif = 19 Motif number = 1
L-type voltage-dependent calcium channel alpha-1 subunit motif I - 2
PCODE ST INT
SNSTNHNLEKVEYAFLIIF CCAD_CHICK 149 149
SNATNSNLERVEYLFLIIF CCAC_HUMAN 152 152
SNATNSNLERVEYLFLIIF CCAC_MOUSE 152 152
SNATNSNLERVEYLFLIIF CCAC_RABIT 182 182
SNATNSNLERVEYLFLIIF CCAC_RAT 182 182
SNSTNHNLEKVEYAFLIIF CCAD_HUMAN 154 154
SNSTNHNLEKVEYAFLIIF CCAD_RAT 154 154
SNSTNHNLEKVEYAFLIIF CCAD_MESAU 153 153
SNATNSNLERVEYLFLIIF Q9Z305 181 181
SNTANHNLEQVEYVFLVIF Q9JIS7 120 120
SNTANHNLEQVEYVFLVIF CCAF_HUMAN 120 120
SNTANHNLEQVEYVFLVIF O95226 55 55
SNTANHNLEQVEYVFLVIF Q9UHB1 120 120
NNTLNLGLEKLEYFFLIVF Q02789 79 79
NNSLNLGLEKLEYFFLIVF CCAS_HUMAN 79 79
NNSLNLGLEKLEYFFLTVF CCAS_RABIT 79 79
TNSTNSVLEKVEYIFLFIF O57483 79 79
TNNTNLTLESLEYIFLVIF CCAS_CYPCA 98 98
LVDCCALPHA12 Length of motif = 12 Motif number = 2
L-type voltage-dependent calcium channel alpha-1 subunit motif II - 2
PCODE ST INT
VVVGLFSVILEQ CCAD_CHICK 200 32
VVVGLFSAILEQ CCAC_HUMAN 203 32
VVVGLFSAILEQ CCAC_MOUSE 203 32
VVVGLFSAILEQ CCAC_RABIT 233 32
VVVGLFSAILEQ CCAC_RAT 233 32
VIVGLFSVILEQ CCAD_HUMAN 205 32
VIVGLFSVILEQ CCAD_RAT 205 32
VIVGLFSVILEQ CCAD_MESAU 204 32
VVVGLFSAILEQ Q9Z305 232 32
VVVGLFSVLLEQ Q9JIS7 171 32
VVVGLFSVLLEQ CCAF_HUMAN 171 32
VVVGLFSVLLEQ O95226 106 32
VVVGLFSVLLEQ Q9UHB1 171 32
VFLGVFTVILEQ Q02789 130 32
VFLGVFTVILEQ CCAS_HUMAN 130 32
VFLGVFTAILEQ CCAS_RABIT 130 32
VSVGVFSVLLEQ O57483 130 32
VFMGLFTLVVDT CCAS_CYPCA 149 32
LVDCCALPHA13 Length of motif = 14 Motif number = 3
L-type voltage-dependent calcium channel alpha-1 subunit motif III - 2
PCODE ST INT
KAKARGDFQKLREK CCAD_CHICK 410 198
KAKARGDFQKLREK CCAC_HUMAN 414 199
KAKARGDFQKLREK CCAC_MOUSE 414 199
KAKARGDFQKLREK CCAC_RABIT 444 199
KAKARGDFQKLREK CCAC_RAT 444 199
KAKARGDFQKLREK CCAD_HUMAN 415 198
KAKARGDFQKLREK CCAD_RAT 415 198
KAKARGDFQKLREN CCAD_MESAU 414 198
KAKARGDFQKLREK Q9Z305 443 199
KAKARGDFQKLREK Q9JIS7 381 198
KAKARGDFQKQREK CCAF_HUMAN 381 198
KAKARGDFQKQREK O95226 316 198
KAKARGDFQKQREK Q9UHB1 381 198
KAKSRGTFQKLREK Q02789 343 201
KAKSRGTFQKLREK CCAS_HUMAN 343 201
KAKSRGTFQKLREK CCAS_RABIT 343 201
KAKSRGAFQMLREQ O57483 341 199
ESRSRGEYQKLRER CCAS_CYPCA 360 199
LVDCCALPHA14 Length of motif = 19 Motif number = 4
L-type voltage-dependent calcium channel alpha-1 subunit motif IV - 2
PCODE ST INT
KFSRRWRRWNRFNRRKCRA CCAD_CHICK 521 97
KFSRYWRRWNRFCRRKCRA CCAC_HUMAN 501 73
KFSRYWRRWNRFCRRKCRA CCAC_MOUSE 501 73
KFSRYWRRWNRFCRRKCRA CCAC_RABIT 531 73
KFSRYWRRWNRFCRRKCRA CCAC_RAT 531 73
KLSRRWRRWNRFNRRRCRA CCAD_HUMAN 500 71
PYSRRWRRWNRFNRRRCRA CCAD_RAT 559 130
KLSRRWRRWNRFNRRRCRA CCAD_MESAU 499 71
KFSRYWRRWNRFCRRKCRA Q9Z305 530 73
RICRHFRRANRGLRARCRR Q9JIS7 506 111
RVCRRLRRANRVLRARCRR CCAF_HUMAN 495 100
RVCRRLRRANRVLRARCRR O95226 441 111
RVCRRLRRANRVLRARCRR Q9UHB1 506 111
QFIRHWRQWNRVFRWKCHD Q02789 409 52
QFIRHWRQWNRIFRWKCHD CCAS_HUMAN 409 52
QFIRHWRQWNRVFRWKCHD CCAS_RABIT 409 52
AFFRQWRLWHRLLRRKSRD O57483 408 53
YFYRLARRWNVVLRRKCHV CCAS_CYPCA 424 50
LVDCCALPHA15 Length of motif = 16 Motif number = 5
L-type voltage-dependent calcium channel alpha-1 subunit motif V - 2
PCODE ST INT
RFDCFVVCGGIVETIL CCAD_CHICK 610 70
RFDCFVVCGGILETIL CCAC_HUMAN 590 70
RFDCFIVCGGILETIL CCAC_MOUSE 590 70
RFDCFIVCGGILETIL CCAC_RABIT 620 70
RFDCFIVCGGILETIL CCAC_RAT 620 70
RFDCFVVCGGITETIL CCAD_HUMAN 589 70
RFDCFVVCGGITETIL CCAD_RAT 648 70
RFDCFVVCGGITETIL CCAD_MESAU 588 70
RLDCFIVCGGILETIL Q9Z305 619 70
RFDCFVVCGGILETTL Q9JIS7 595 70
RFDCFVVCGGILETTL CCAF_HUMAN 584 70
RFDCFVVCGGILETTL O95226 530 70
RFDCFVVCGGILETTL Q9UHB1 595 70
RFDCFVVCSGILEILL Q02789 498 70
RFDCFVVCSGILEILL CCAS_HUMAN 498 70
RFDCFVVCSGILELLL CCAS_RABIT 498 70
RFDSFVVCTGLLEVML O57483 497 70
RFDCFVVTIGILEIIL CCAS_CYPCA 513 70
LVDCCALPHA16 Length of motif = 14 Motif number = 6
L-type voltage-dependent calcium channel alpha-1 subunit motif VI - 2
PCODE ST INT
NFDETQTKRSTFDN CCAD_CHICK 698 72
NFDEMQTRRSTFDN CCAC_HUMAN 678 72
NFDEMQTRRSTFDN CCAC_MOUSE 678 72
NFDEMQTRRSTFDN CCAC_RABIT 708 72
NFDEMQTRRSTFDN CCAC_RAT 708 72
NFDETQTKRSTFDN CCAD_HUMAN 677 72
NFDETQTKRSTFDN CCAD_RAT 736 72
NFDETQTKRSTFDN CCAD_MESAU 676 72
NFDEMRTRRSTFDN Q9Z305 707 72
NFDQTHTKRSTFDT Q9JIS7 683 72
NFDQTHTKRSTFDT CCAF_HUMAN 672 72
NFDQTHTKRSTFDT O95226 618 72
NFDQTHTKRSTFDT Q9UHB1 683 72
DFEDTEVRRSNFDN Q02789 586 72
DFEDTEVRRSNFDN CCAS_HUMAN 586 72
DFEDTEVRRSNFDN CCAS_RABIT 586 72
DFEDLEVRRSTFDT O57483 585 72
NFPDRVIQRSNFDN CCAS_CYPCA 601 72
User query: Display/Full Code "LVDCCALPHA1"