WORKLIST ENTRIES (1):
TVDCCALPHA1 View alignment T-type voltage-dependent calcium channel alpha-1 subunit signature
Type of fingerprint: COMPOUND with 5 elements
Links:
PRINTS; PR00167 CACHANNEL; PR01630 LVDCCALPHA1; PR01631 NVDCCALPHA1
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. CRIBBS, L., LEE, J.H., YANG, J., SATIN, J., ZHANG, Y., DAUD, A.,
BARCLAY, J., WILLIAMSON, M.P., FOX, M., REES, M. AND PEREZ-REYES, E.
Cloning and characterization of alpha1H from human heart, a member of the
T-type Ca2+ channel gene family.
CIRC.RES. 83 103-109 (1998).
6. HUGUENARD, J.R.
Low-threshold calcium currents in central nervous system neurons.
ANNU.REV.PHYSIOL. 58 329-348 (1996).
7. ENYEART, J.J., MLINAR, B. AND ENYEART, J.A.
T-type Ca2+ channels are required for adrenocorticotropin-stimulated
cortisol production by bovine adrenal zona fasciculata cells.
MOL.ENDOCRINOL. 7 1031-1040 (1993).
8. AKAIKE, N., KOSTYUK, P.G. AND OSIPCHUK, Y.V.
Dihydropyridine-sensitive low-threshold calcium channels in isolated rat
hypothalamic neurones.
J.PHYSIOL. 412 181-195 (1989).
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]. T-type calcium channels are
composed of alpha-1G and alpha-1H subunits [5]. They exhibit unique voltage-
dependent kinetics, small single channel conductance, rapid inactivation,
slow deactivation and a relatively high permeability to calcium [6]. They
are primarily responsible for rebound burst firing in central neurons and
are implicated in normal brain functions, such as slow wave sleep, and in
diseased states, such as epilepsy [6]. They also play an important role in
hormone secretion [7] and smooth muscle excitability [8].
TVDCCALPHA1 is a 5-element fingerprint that provides a signature for the
T-type voltage-dependent calcium channel alpha-1 subunit. The fingerprint
was derived from an initial alignment of 6 sequences: the motifs were drawn
from conserved regions spanning the full alignment length: motif 1 lies in
the cytoplasmic N-terminus; motif 2 resides in the extracellular region
between TM domains 1 and 2 of repeat I; motif 3 spans the cytoplasmic region
between TM domain 6 of repeat I and TM domain 1 of repeat II; motif 4
spans part of TM domain 1 of repeat II and the following extracellular
region; and motif 5 lies in the cytoplasmic region between TM domain 6 of
repeat III and domain I in repeat IV. Two iterations on SPTR40_18f were
required to reach convergence, at which point a true set comprising 12
sequences was identified. A single partial match was also found, Q9W433,
a family member from Drosophila that fails to make significant matches with
motifs 1 and 5.
SUMMARY INFORMATION
12 codes involving 5 elements
0 codes involving 4 elements
1 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
5| 12 12 12 12 12
4| 0 0 0 0 0
3| 0 1 1 1 0
2| 0 0 0 0 0
--+--------------------------
| 1 2 3 4 5
True positives..
Q9NZC8 Q9UNE6 Q9P0X4 Q9EQ59
CCAI_RAT CCAG_HUMAN CCAG_RAT Q9WUB8
Q9WUT2 Q9EQ60 CCAH_HUMAN Q9JKU5
Subfamily: Codes involving 3 elements
Subfamily True positives..
Q9W433
PROTEIN TITLES
Q9NZC8 T-TYPE CALCIUM CHANNEL ALPHA1 SUBUNIT ALPHA1I-A ISOFORM - Ho
Q9UNE6 T-TYPE CALCIUM CHANNEL ALPHA1I SUBUNIT - Homo sapiens (Human
Q9P0X4 T CALCIUM CHANNEL ALPHA1I SUBUNIT, DELTA36B SPLICE VARIANT -
Q9EQ59 CALCIUM CHANNEL ALPHA-1-I SUBUNIT - Rattus norvegicus (Rat).
CCAI_RAT Voltage-dependent T-type calcium channel alpha-1I subunit (C
CCAG_HUMAN Voltage-dependent T-type calcium channel alpha-1G subunit (N
CCAG_RAT Voltage-dependent T-type calcium channel alpha-1G subunit -
Q9WUB8 T-TYPE CALCIUM CHANNEL ISOFORM - Rattus norvegicus (Rat).
Q9WUT2 VOLTAGE-GATED CALCIUM CHANNEL, ALPHA-1-G SUBUNIT - Mus muscu
Q9EQ60 CALCIUM CHANNEL ALPHA-1-H SUBUNIT - Rattus norvegicus (Rat).
CCAH_HUMAN Voltage-dependent T-type calcium channel alpha-1H subunit -
Q9JKU5 LOW-VOLTAGE-ACTIVATED CALCIUM CHANNEL ALPHA13.2 SUBUNIT - Mu
Q9W433 CG4222 PROTEIN - Drosophila melanogaster (Fruit fly).
SCAN HISTORY
SPTR40_18f 2 100 NSINGLE
INITIAL MOTIF SETS
TVDCCALPHA11 Length of motif = 17 Motif number = 1
T-type voltage-dependent calcium channel alpha-1 subunit motif I - 1
PCODE ST INT
FFYLSQDSRPRSWCLRT CCAG_HUMAN 61 61
FFYLSQDSRPRSWCLRT CCAG_RAT 61 61
FFCLGQTTRPRSWCLRL CCAH_HUMAN 80 80
FFCLRQTTSPRNWCIKM CCAI_RAT 57 57
FFCLRQTTSPRNWCIKM Q9UNE6 59 59
FFCLRQTTSPRNWCIKM Q9EQ59 57 57
TVDCCALPHA12 Length of motif = 17 Motif number = 2
T-type voltage-dependent calcium channel alpha-1 subunit motif II - 1
PCODE ST INT
PCEDIACDSQRCRILQA CCAG_HUMAN 103 25
PCEDIACDSQRCRILQA CCAG_RAT 103 25
PCEDVECGSERCNILEA CCAH_HUMAN 122 25
PCDDMECLSDRCKILQV CCAI_RAT 99 25
PCDDMDCLSDRCKILQV Q9UNE6 101 25
PCDDMECLSDRCKILQV Q9EQ59 99 25
TVDCCALPHA13 Length of motif = 15 Motif number = 3
T-type voltage-dependent calcium channel alpha-1 subunit motif III - 1
PCODE ST INT
EPGSCYEELLKYLVY CCAG_HUMAN 428 308
EPGSCYEELLKYLVY CCAG_RAT 428 308
EPGSCYEELLKYVGH CCAH_HUMAN 452 313
EPGDCYEEIFQYVCH CCAI_RAT 428 312
EPGDCYEEIFQYVCH Q9UNE6 430 312
EPGDCYEEIFQYVCH Q9EQ59 428 312
TVDCCALPHA14 Length of motif = 14 Motif number = 4
T-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1
PCODE ST INT
GIEYHEQPEELTNA CCAG_HUMAN 761 318
GIEYHEQPEELTNA CCAG_RAT 762 319
GVEYHEQPEELTNA CCAH_HUMAN 811 344
GIEHHEQPEELTNI CCAI_RAT 616 173
GIEHHEQPEELTNI Q9UNE6 658 213
GIEHHEQPEELTNI Q9EQ59 616 173
TVDCCALPHA15 Length of motif = 16 Motif number = 5
T-type voltage-dependent calcium channel alpha-1 subunit motif V - 1
PCODE ST INT
EEEEARRREEKRLRRL CCAG_HUMAN 1548 773
EEEEARRREEKRLRRL CCAG_RAT 1527 751
EAEEARRREEKRLRRL CCAH_HUMAN 1566 741
EAEEARRREEKRLRRL CCAI_RAT 1401 771
EAEEARRREEKRLRRL Q9UNE6 1442 770
EAEEARRREEKRLRRL Q9EQ59 1400 770
FINAL MOTIF SETS
TVDCCALPHA11 Length of motif = 17 Motif number = 1
T-type voltage-dependent calcium channel alpha-1 subunit motif I - 2
PCODE ST INT
FFCLRQTTSPRNWCIKM Q9NZC8 59 59
FFCLRQTTSPRNWCIKM Q9UNE6 59 59
FFCLRQTTSPRNWCIKM Q9P0X4 59 59
FFCLRQTTSPRNWCIKM CCAI_RAT 57 57
FFCLRQTTSPRNWCIKM Q9EQ59 57 57
FFYLSQDSRPRSWCLRT CCAG_HUMAN 61 61
FFYLSQDSRPRSWCLRT CCAG_RAT 61 61
FFYLSQDSRPRSWCLRT Q9WUB8 61 61
FFYLSQDSRPRSWCLRT Q9WUT2 61 61
FFCLGQTTRPRSWCLRL CCAH_HUMAN 80 80
FFCLGQTTRPRSWCLRL Q9EQ60 80 80
FFCLGQTTRPRSWCLRL Q9JKU5 80 80
TVDCCALPHA12 Length of motif = 17 Motif number = 2
T-type voltage-dependent calcium channel alpha-1 subunit motif II - 2
PCODE ST INT
PCDDMDCLSDRCKILQV Q9NZC8 101 25
PCDDMDCLSDRCKILQV Q9UNE6 101 25
PCDDMDCLSDRCKILQV Q9P0X4 101 25
PCDDMECLSDRCKILQV CCAI_RAT 99 25
PCDDMECLSDRCKILQV Q9EQ59 99 25
PCEDIACDSQRCRILQA CCAG_HUMAN 103 25
PCEDIACDSQRCRILQA CCAG_RAT 103 25
PCEDIACDSQRCRILQA Q9WUB8 103 25
PCEDIACDSQRCRILQA Q9WUT2 103 25
PCEDVECGSERCNILEA CCAH_HUMAN 122 25
PCEDVECRSERCSILEA Q9EQ60 122 25
PCEDVECRSERCSILEA Q9JKU5 122 25
TVDCCALPHA13 Length of motif = 15 Motif number = 3
T-type voltage-dependent calcium channel alpha-1 subunit motif III - 2
PCODE ST INT
EPGDCYEEIFQYVCH Q9NZC8 430 312
EPGDCYEEIFQYVCH Q9UNE6 430 312
EPGDCYEEIFQYVCH Q9P0X4 430 312
EPGDCYEEIFQYVCH CCAI_RAT 428 312
EPGDCYEEIFQYVCH Q9EQ59 428 312
EPGSCYEELLKYLVY CCAG_HUMAN 428 308
EPGSCYEELLKYLVY CCAG_RAT 428 308
EPGSCYEELLKYLVY Q9WUB8 428 308
EPGSCYEELLKYLVY Q9WUT2 428 308
EPGSCYEELLKYVGH CCAH_HUMAN 452 313
EPGSCYEELLKYVGH Q9EQ60 452 313
EPGSCYEELLKYVGH Q9JKU5 452 313
TVDCCALPHA14 Length of motif = 14 Motif number = 4
T-type voltage-dependent calcium channel alpha-1 subunit motif IV - 2
PCODE ST INT
GIEHHEQPEELTNI Q9NZC8 623 178
GIEHHEQPEELTNI Q9UNE6 658 213
GIEHHEQPEELTNI Q9P0X4 658 213
GIEHHEQPEELTNI CCAI_RAT 616 173
GIEHHEQPEELTNI Q9EQ59 616 173
GIEYHEQPEELTNA CCAG_HUMAN 761 318
GIEYHEQPEELTNA CCAG_RAT 762 319
GIEYHEQPEELTNA Q9WUB8 762 319
GIEYHEQPEELTNA Q9WUT2 761 318
GVEYHEQPEELTNA CCAH_HUMAN 811 344
GVEYHEQPEELTNA Q9EQ60 808 341
GVEYHEQPDELTNA Q9JKU5 808 341
TVDCCALPHA15 Length of motif = 16 Motif number = 5
T-type voltage-dependent calcium channel alpha-1 subunit motif V - 2
PCODE ST INT
EAEEARRREEKRLRRL Q9NZC8 1407 770
EAEEARRREEKRLRRL Q9UNE6 1442 770
EAEEARRREEKRLRRL Q9P0X4 1442 770
EAEEARRREEKRLRRL CCAI_RAT 1401 771
EAEEARRREEKRLRRL Q9EQ59 1400 770
EEEEARRREEKRLRRL CCAG_HUMAN 1548 773
EEEEARRREEKRLRRL CCAG_RAT 1527 751
EEEEARRREEKRLRRL Q9WUB8 1550 774
EEEEARRREEKRLKRL Q9WUT2 1549 774
EAEEARRREEKRLRRL CCAH_HUMAN 1566 741
EAEEARRREEKRLRRL Q9EQ60 1577 755
EAEEARRREEKRLRRL Q9JKU5 1577 755
User query: Display/Full Code "TVDCCALPHA1"