WORKLIST ENTRIES (1):
NVDCCALPHA1 View alignment N-type voltage-dependent calcium channel alpha-1 subunit signature
Type of fingerprint: COMPOUND with 7 elements
Links:
PRINTS; PR00167 CACHANNEL; PR01629 TVDCCALPHA1; PR01630 LVDCCALPHA1
PRINTS; PR01632 PQVDCCALPHA1; PR01633 RVDCCALPHA1
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. LUEBKE, J.I., DUNLAP, K. AND TURNER, T.J.
Multiple calcium channel types control glutamatergic synaptic transmission
in the hippocampus.
NEURON 11 895-902 (1993).
6. TURNER, T.J., ADAMS, M.E. AND DUNLAP, K.
Multiple Ca2+ channel types coexist to regulate synaptosomal
neurotransmitter release.
PROC.NATL.ACAD.SCI.U.S.A. 90 9518-9522 (1993).
7. HIRNING, L.D., FOX, A.P., MCCLESKEY, E.W., OLIVERA, B.M., THAYER, S.A.,
MILLER, R.J. AND TSIEN, R.E.
Dominant role of N-type Ca2+ channels in evoked release of norepinephrine
from sympathetic neurons.
SCIENCE 239 57-61 (1988).
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]. N-type calcium channels are
composed from alpha-1B subunits. Experiments employing CTX have demonstrated
the physiological importance of the N-type calcium channels in the nervous
system, where they have a significant developmental role in the migration
of immature neurons before the establishment of their synaptic circuit. In
peripheral neurons, such as autonomic neurons, motor neurons and spinal
cord neurons, they have also been shown to be critically involved in the
release of neurotransmitters, including glutamate [5], gamma-amino-butyric
acid, acetylcholine, dopamine [6] and norepinephrine [7].
NVDCCALPHA1 is a 7-element fingerprint that provides a signature for the
N-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 full alignment length: motif 1 lies in
the extracellular region between TM domains 5 and 6 of repeat I; motifs 2-6
encode the cytoplasmic region between the sixth TM domain of repeat II and
TM domain 1 of repeat III; and motif 7 resides in the cytoplasmic C-terminus.
Two iterations on SPTR40_18f were required to reach convergence, at which
point a true set comprising 15 sequences was identified.
SUMMARY INFORMATION
15 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
7| 15 15 15 15 15 15 15
6| 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0
2| 0 0 0 0 0 0 0
--+------------------------------------
| 1 2 3 4 5 6 7
True positives..
CCAB_RABIT CCAB_HUMAN CCAB_RAT O89089
Q9TTA4 CCAB_MOUSE CCAB_DISOM Q9PUM3
Q9PW47 Q9PW46 Q9PW45 Q9PW44
Q9PUM6 Q9PUM5 Q9PUM4
PROTEIN TITLES
CCAB_RABIT Voltage-dependent N-type calcium channel alpha-1B subunit (C
CCAB_HUMAN Voltage-dependent N-type calcium channel alpha-1B subunit (C
CCAB_RAT Voltage-dependent N-type calcium channel alpha-1B subunit (C
O89089 PORE-FORMING CALCIUM CHANNEL ALPHA-1B SUBUNIT VARIANT A - Ra
Q9TTA4 N-TYPE CALCIUM CHANNEL ALPHA1B SUBUNIT - Bos taurus (Bovine)
CCAB_MOUSE Voltage-dependent N-type calcium channel alpha-1B subunit (C
CCAB_DISOM Probable voltage-dependent N-type calcium channel alpha-1B s
Q9PUM3 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB4 VARIANT - Gallus gallus
Q9PW47 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB5 VARIANT - Gallus gallus
Q9PW46 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB6 VARIANT - Gallus gallus
Q9PW45 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB7 VARIANT - Gallus gallus
Q9PW44 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB8 VARIANT - Gallus gallus
Q9PUM6 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB1 VARIANT - Gallus gallus
Q9PUM5 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB2 VARIANT - Gallus gallus
Q9PUM4 N-TYPE CALCIUM CHANNEL ALPHA-1B CDB3 VARIANT - Gallus gallus
SCAN HISTORY
SPTR40_18f 2 150 NSINGLE
INITIAL MOTIF SETS
NVDCCALPHA11 Length of motif = 13 Motif number = 1
N-type voltage-dependent calcium channel alpha-1 subunit motif I - 1
PCODE ST INT
EPVGDFPCGKEAP CCAB_HUMAN 261 261
EPVGDFPCGKDPP CCAB_MOUSE 261 261
DPVGDFPCGKEAP CCAB_RABIT 261 261
EPVEEFPCGTKYP CCAB_DISOM 253 253
DPVGDFPCGREAP Q9TTA4 261 261
NVDCCALPHA12 Length of motif = 14 Motif number = 2
N-type voltage-dependent calcium channel alpha-1 subunit motif II - 1
PCODE ST INT
LRLQNLRASCEALY CCAB_HUMAN 775 501
LRLQNLRASCEALY CCAB_MOUSE 775 501
LRLQNLRASCEALY CCAB_RABIT 776 502
LRRQHILTSQEALF CCAB_DISOM 766 500
LRLQNLRASCEALY Q9TTA4 775 501
NVDCCALPHA13 Length of motif = 17 Motif number = 3
N-type voltage-dependent calcium channel alpha-1 subunit motif III - 1
PCODE ST INT
APEGVDPPRRHHRHRDK CCAB_HUMAN 841 52
ATESADLPRRHHRHRDR CCAB_MOUSE 841 52
APEGADPPRRHHRHRDK CCAB_RABIT 842 52
QPESCEAPRRSHRHRDK CCAB_DISOM 838 58
AGEGADPPRRHHRHRDR Q9TTA4 841 52
NVDCCALPHA14 Length of motif = 12 Motif number = 4
N-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1
PCODE ST INT
RHHRRGSPEEAA CCAB_HUMAN 917 59
RHHRRGSPEEAT CCAB_MOUSE 909 51
RHHRRGSPEEAA CCAB_RABIT 922 63
HHHAQSSLDDAP CCAB_DISOM 912 57
RHHRRGSPEEAA Q9TTA4 920 62
NVDCCALPHA15 Length of motif = 16 Motif number = 5
N-type voltage-dependent calcium channel alpha-1 subunit motif V - 1
PCODE ST INT
PSTCLQKVEEQPEDAD CCAB_HUMAN 1044 115
PSTCLQKVDEQPEDAD CCAB_MOUSE 1033 112
PSTCLQKVEEQPEDAD CCAB_RABIT 1049 115
PPIGLQHLPQQPEDAD CCAB_DISOM 1035 111
PSTCLEKVEEQPEDAD Q9TTA4 1037 105
NVDCCALPHA16 Length of motif = 17 Motif number = 6
N-type voltage-dependent calcium channel alpha-1 subunit motif VI - 1
PCODE ST INT
TIVHIPVMLTGPLGEAT CCAB_HUMAN 1076 16
TTVHVPVTLTGPPGETP CCAB_MOUSE 1065 16
TTVHIPVTLTGPPGETT CCAB_RABIT 1081 16
ATVNIPVTVTTPAAEMT CCAB_DISOM 1069 18
TAVRIPVTLTGPPGETT Q9TTA4 1069 16
NVDCCALPHA17 Length of motif = 20 Motif number = 7
N-type voltage-dependent calcium channel alpha-1 subunit motif VII - 1
PCODE ST INT
HHHRCHRRRDRKQRSLEKGP CCAB_HUMAN 2052 959
HHHRCHRRRDKKQRSLEKGP CCAB_MOUSE 2042 960
HHHRCHRRRDRKQRSLEKGP CCAB_RABIT 2053 955
HHHRCHHRREKKQRSLERAT CCAB_DISOM 2044 958
HHHRCHRRRDRKQKSLEKGP Q9TTA4 2042 956
FINAL MOTIF SETS
NVDCCALPHA11 Length of motif = 13 Motif number = 1
N-type voltage-dependent calcium channel alpha-1 subunit motif I - 2
PCODE ST INT
DPVGDFPCGKEAP CCAB_RABIT 261 261
EPVGDFPCGKEAP CCAB_HUMAN 261 261
EPVGDFPCGKEAP CCAB_RAT 261 261
EPVGDFPCGKEAP O89089 261 261
DPVGDFPCGREAP Q9TTA4 261 261
EPVGDFPCGKDPP CCAB_MOUSE 261 261
EPVEEFPCGTKYP CCAB_DISOM 253 253
EEVGDFPCGEEPP Q9PUM3 252 252
EEVGDFPCGEEPP Q9PW47 252 252
EEVGDFPCGEEPP Q9PW46 252 252
EEVGDFPCGEEPP Q9PW45 252 252
EEVGDFPCGEEPP Q9PW44 252 252
EEVGDFPCGEEPP Q9PUM6 252 252
EEVGDFPCGEEPP Q9PUM5 252 252
EEVGDFPCGEEPP Q9PUM4 252 252
NVDCCALPHA12 Length of motif = 14 Motif number = 2
N-type voltage-dependent calcium channel alpha-1 subunit motif II - 2
PCODE ST INT
LRLQNLRASCEALY CCAB_RABIT 776 502
LRLQNLRASCEALY CCAB_HUMAN 775 501
LRLQNLRASCEALY CCAB_RAT 776 502
LRLQNLRASCEALY O89089 775 501
LRLQNLRASCEALY Q9TTA4 775 501
LRLQNLRASCEALY CCAB_MOUSE 775 501
LRRQHILTSQEALF CCAB_DISOM 766 500
IRMHNFRASCEALY Q9PUM3 755 490
IRMHNFRASCEALY Q9PW47 780 515
IRMHNFRASCEALY Q9PW46 780 515
IRMHNFRASCEALY Q9PW45 766 501
IRMHNFRASCEALY Q9PW44 766 501
IRMHNFRASCEALY Q9PUM6 791 526
IRMHNFRASCEALY Q9PUM5 791 526
IRMHNFRASCEALY Q9PUM4 755 490
NVDCCALPHA13 Length of motif = 17 Motif number = 3
N-type voltage-dependent calcium channel alpha-1 subunit motif III - 2
PCODE ST INT
APEGADPPRRHHRHRDK CCAB_RABIT 842 52
APEGVDPPRRHHRHRDK CCAB_HUMAN 841 52
ATEGADPPRRHHRHRDR CCAB_RAT 842 52
ATEGADPPRRHHRHRDR O89089 841 52
AGEGADPPRRHHRHRDR Q9TTA4 841 52
ATESADLPRRHHRHRDR CCAB_MOUSE 841 52
QPESCEAPRRSHRHRDK CCAB_DISOM 838 58
STDGAEAPRKHHRHRDK Q9PUM3 827 58
STDGAEAPRKHHRHRDK Q9PW47 852 58
STDGAEAPRKHHRHRDK Q9PW46 852 58
STDGAEAPRKHHRHRDK Q9PW45 838 58
STDGAEAPRKHHRHRDK Q9PW44 838 58
STDGAEAPRKHHRHRDK Q9PUM6 863 58
STDGAEAPRKHHRHRDK Q9PUM5 863 58
STDGAEAPRKHHRHRDK Q9PUM4 827 58
NVDCCALPHA14 Length of motif = 12 Motif number = 4
N-type voltage-dependent calcium channel alpha-1 subunit motif IV - 2
PCODE ST INT
RHHRRGSPEEAA CCAB_RABIT 922 63
RHHRRGSPEEAA CCAB_HUMAN 917 59
RHHRRGSPEEAT CCAB_RAT 915 56
RHHRRGSPEEAT O89089 914 56
RHHRRGSPEEAA Q9TTA4 920 62
RHHRRGSPEEAT CCAB_MOUSE 909 51
HHHAQSSLDDAP CCAB_DISOM 912 57
RHHRRGSVEEGV Q9PUM3 901 57
RHHRRGSVEEGV Q9PW47 926 57
RHHRRGSVEEGV Q9PW46 926 57
RHHRRGSVEEGV Q9PW45 912 57
RHHRRGSVEEGV Q9PW44 912 57
RHHRRGSVEEGV Q9PUM6 937 57
RHHRRGSVEEGV Q9PUM5 937 57
RHHRRGSVEEGV Q9PUM4 901 57
NVDCCALPHA15 Length of motif = 16 Motif number = 5
N-type voltage-dependent calcium channel alpha-1 subunit motif V - 2
PCODE ST INT
PSTCLQKVEEQPEDAD CCAB_RABIT 1049 115
PSTCLQKVEEQPEDAD CCAB_HUMAN 1044 115
PSTCLQKVDEQPEDAD CCAB_RAT 1042 115
PSTCLQKVDEQPEDAD O89089 1041 115
PSTCLEKVEEQPEDAD Q9TTA4 1037 105
PSTCLQKVDEQPEDAD CCAB_MOUSE 1033 112
PPIGLQHLPQQPEDAD CCAB_DISOM 1035 111
PSTYLQKVPEQPEDAD Q9PUM3 1030 117
PSTYLQKVPEQPEDAD Q9PW47 1055 117
PSTYLQKVPEQPEDAD Q9PW46 1055 117
PSTYLQKVPEQPEDAD Q9PW45 1041 117
PSTYLQKVPEQPEDAD Q9PW44 1041 117
PSTYLQKVPEQPEDAD Q9PUM6 1066 117
PSTYLQKVPEQPEDAD Q9PUM5 1066 117
PSTYLQKVPEQPEDAD Q9PUM4 1030 117
NVDCCALPHA16 Length of motif = 17 Motif number = 6
N-type voltage-dependent calcium channel alpha-1 subunit motif VI - 2
PCODE ST INT
TTVHIPVTLTGPPGETT CCAB_RABIT 1081 16
TIVHIPVMLTGPLGEAT CCAB_HUMAN 1076 16
TTVHVPVTLTGPPGEAT CCAB_RAT 1074 16
TTVHVPVTLTGPPGEAT O89089 1073 16
TAVRIPVTLTGPPGETT Q9TTA4 1069 16
TTVHVPVTLTGPPGETP CCAB_MOUSE 1065 16
ATVNIPVTVTTPAAEMT CCAB_DISOM 1069 18
TTVNIPVTITAPPGETT Q9PUM3 1062 16
TTVNIPVTITAPPGETT Q9PW47 1087 16
TTVNIPVTITAPPGETT Q9PW46 1087 16
TTVNIPVTITAPPGETT Q9PW45 1073 16
TTVNIPVTITAPPGETT Q9PW44 1073 16
TTVNIPVTITAPPGETT Q9PUM6 1098 16
TTVNIPVTITAPPGETT Q9PUM5 1098 16
TTVNIPVTITAPPGETT Q9PUM4 1062 16
NVDCCALPHA17 Length of motif = 20 Motif number = 7
N-type voltage-dependent calcium channel alpha-1 subunit motif VII - 2
PCODE ST INT
HHHRCHRRRDRKQRSLEKGP CCAB_RABIT 2053 955
HHHRCHRRRDRKQRSLEKGP CCAB_HUMAN 2052 959
HHHRCHRRRDKKQRSLEKGP CCAB_RAT 2051 960
HHHRCHRRRDKKQRSLEKGP O89089 2048 958
HHHRCHRRRDRKQKSLEKGP Q9TTA4 2042 956
HHHRCHRRRDKKQRSLEKGP CCAB_MOUSE 2042 960
HHHRCHHRREKKQRSLERAT CCAB_DISOM 2044 958
HHHRCHRRKEKKQKSLDRTT Q9PUM3 2045 966
HHHRCHRRKEKKQKSLDRTT Q9PW47 2070 966
HHHRCHRRKEKKQKSLDRTT Q9PW46 2070 966
HHHRCHRRKEKKQKSLDRTT Q9PW45 2056 966
HHHRCHRRKEKKQKSLDRTT Q9PW44 2056 966
HHHRCHRRKEKKQKSLDRTT Q9PUM6 2081 966
HHHRCHRRKEKKQKSLDRTT Q9PUM5 2081 966
HHHRCHRRKEKKQKSLDRTT Q9PUM4 2045 966
User query: Display/Full Code "NVDCCALPHA1"