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PR00170

Identifier
NACHANNEL  [View Relations]  [View Alignment]  
Accession
PR00170
No. of Motifs
2
Creation Date
06-MAY-1993  (UPDATE 22-MAY-2000)
Title
Voltage-gated Na+ channel alpha subunit signature
Database References
PRINTS; PR01664 NACHANNEL1; PR01665 NACHANNEL4; PR01666 NACHANNEL5
PRINTS; PR01667 NACHANNEL8
INTERPRO; IPR001696
Literature References
1. GEORGE, A.L., KNITTLE, T.J. AND TAMKUN, M.M.
Molecular cloning of an atypical voltage-gated sodium channel expressed in
human heart and uterus - Evidence for a distinct gene family.
PROC.NATL.ACAD.SCI.U.S.A. 89(11) 4893-4897 (1992).
 
2. NODA, M., IKEDA, T., KAYANO, T., SUZUKI, H., TAKESHIMA, H., 
KURASAKI, M., TAKAHASHI, H. AND NUMA, S.
Existence of distinct sodium channel messenger RNAs in rat brain.
NATURE 320 188-192 (1986).
 
3. NODA, M., SHIMIZU, S., TANABE, T., TAKAI, T., KAYANO, T., IKEDA, T., 
TAKAHASHI, H., NAKAYAMA, H., KANAOKA, Y., MINAMINO, M., KANGAWA, K., 
MATSUO, H., RAFTERY, M.A., HIROSE, T., INAYAMA, S., HAYASHIDA, H, MIYATA,
T. AND NUMA, S.
Primary structure of Electrophorus electricus sodium channel deduced from 
cDNA sequence.
NATURE 312 121-127 (1984).
 
4. ROGART, R.B., CRIBBS, L.L., MUGLIA, L.K., KEPHART, D.D. AND KAISER, M.W.
Molecular cloning of a putative tetrodotoxin resistant rat heart Na+
channel isoform.
PROC.NATL.ACAD.SCI.U.S.A. 86(20) 8170-8174 (1989).
 
5. SATO, C. AND MATSUMOTO, G.
Proposed tertiary structure of the sodium channel.
BIOCHEM.BIOPHYS.RES.COMMUN. 186 1158-1167 (1992).

Documentation
Voltage-dependent sodium channels are transmembrane (TM) proteins
responsible for the depolarising phase of the action potential in most
electrically excitable cells [1]. They may exist in 3 states [3]: the
resting state, where the channel is closed; the activated state, where the
channel is open; and the inactivated state, where the channel is closed
and refractory to opening. Several different structurally and functionally
distinct isoforms are found in mammals, coded for by a multigene family
[4], these being responsible for the different types of sodium ion currents
found in excitable tissues.
 
The structure of sodium channels is based on 4 internal repeats of a
6-helix bundle [2] (in which 5 of the membrane-spanning segments are
hydrophobic and the other is positively charged), forming a 24-helical
bundle. The charged segments are believed to be localised within clusters
formed by their 5 hydrophobic neighbours: it is postulated that the charged
domain may be the voltage sensor region, possibly moving outward on
depolarisation, causing a conformational change. This model, proposed by
Noda et al. [2], contrasts with that of Sato and Matsumoto [5], in which
the TM segments are juxtaposed octagonally. The basic structural motif (the
6-helix bundle) is also found in potassium and calcium channels alpha
subunits.
 
NACHANNEL is a 2-element fingerprint that provides a signature for voltage-
gated Na+ channel alpha subunits. The fingerprint was derived from an
initial alignment of 34 sequences: motif 1 lies on the sixth TM domain, of
the fourth internal repeat; and motif 2 encodes a portion of the putative 
cytoplasmic C-terminus. Two iterations on SPTR37_10f were required to reach
convergence, at which point a true set comprising 49 sequences was
identified.
Summary Information
49 codes involving  2 elements
Composite Feature Index
24949
12
True Positives
CIN1_LOLBL    CIN1_RAT      CIN2_RAT      CIN3_RAT      
CIN4_HUMAN CIN4_RAT CIN5_HUMAN CIN5_RAT
CIN6_HUMAN CINA_DROME CINA_ELEEL O01306
O01307 O02037 O44930 O46669
O62604 O70611 O88420 O88421
O88457 O95788 P70276 P90670
P97706 Q14472 Q15478 Q15858
Q17314 Q24528 Q24529 Q24530
Q24531 Q24532 Q25150 Q25377
Q25439 Q25440 Q28371 Q28644
Q60858 Q62205 Q62243 Q62467
Q62968 Q63541 Q63554 Q94615
Q9YGN7
Sequence Titles
CIN1_LOLBL  SODIUM CHANNEL PROTEIN I, BRAIN - LOLIGO BLEEKERI (BLEEKER'S SQUID). 
CIN1_RAT Sodium channel protein, brain I alpha subunit - Rattus norvegicus (Rat).
CIN2_RAT SODIUM CHANNEL PROTEIN, BRAIN II ALPHA SUBUNIT - RATTUS NORVEGICUS (RAT).
CIN3_RAT SODIUM CHANNEL PROTEIN, BRAIN III ALPHA SUBUNIT - RATTUS NORVEGICUS (RAT).
CIN4_HUMAN Sodium channel protein, skeletal muscle alpha-subunit - Homo sapiens (Human).
CIN4_RAT Sodium channel protein, skeletal muscle alpha-subunit (MU-1) - Rattus norvegicus (Rat).
CIN5_HUMAN Sodium channel protein, cardiac muscle alpha-subunit (HH1) - Homo sapiens (Human).
CIN5_RAT Sodium channel protein, cardiac muscle alpha-subunit - Rattus norvegicus (Rat).
CIN6_HUMAN SODIUM CHANNEL PROTEIN, CARDIAC AND SKELETAL MUSCLE ALPHA-SUBUNIT - HOMO SAPIENS (HUMAN).
CINA_DROME SODIUM CHANNEL PROTEIN PARA (PARALYTIC PROTEIN) - DROSOPHILA MELANOGASTER (FRUIT FLY).
CINA_ELEEL SODIUM CHANNEL PROTEIN (NA+ CHANNEL) - ELECTROPHORUS ELECTRICUS (ELECTRIC EEL).
O01306 PARA SODIUM CHANNEL - BLATTELLA GERMANICA (GERMAN COCKROACH).
O01307 PARA SODIUM CHANNEL - BLATTELLA GERMANICA (GERMAN COCKROACH).
O02037 VOLTAGE-GATED SODIUM CHANNEL HOMOLOG BDNA1 - BDELLOURA CANDIDA.
O44930 PUTATIVE VOLTAGE-GATED SODIUM CHANNEL - AIPTASIA PALLIDA.
O46669 TTX-RESISTANT SODIUM CHANNEL - CANIS FAMILIARIS (DOG).
O62604 VOLTAGE-GATED SODIUM CHANNEL ALPHA SUBUNIT - POLYORCHIS PENICILLATUS (HYDROMEDUSA).
O70611 RAT SKELETAL MUSCLE TYPE 1 VOLTAGE-GATED SODIUM CHANNEL (RSKM1) VARIANT (RSKM1) - Rattus norvegicus (Rat).
O88420 VOLTAGE-GATED SODIUM CHANNEL RPN4 - Rattus norvegicus (Rat).
O88421 VOLTAGE-GATED SODIUM CHANNEL VARIANT RPN4A - Rattus norvegicus (Rat).
O88457 VOLTAGE-GATED NA CHANNEL ALPHA SUBUNIT NAN - RATTUS NORVEGICUS (RAT).
O95788 VOLTAGE-GATED SODIUM CHANNEL ALPHA SUBUNIT - Homo sapiens (Human).
P70276 SODIUM CHANNEL, TYPE X, ALPHA POLYPEPTIDE (VOLTAGE-GATED SODIUM CHANNEL) - MUS MUSCULUS (MOUSE).
P90670 SODIUM CHANNEL ALPHA-SUBUNIT SCAP1 - APLYSIA CALIFORNICA (CALIFORNIA SEA HARE).
P97706 SODIUM CHANNEL - RATTUS NORVEGICUS (RAT).
Q14472 VOLTAGE-GATED SODIUM CHANNEL (VOLTAGE-GATED SODIUM CHANNEL SUBTYPE II) - HOMO SAPIENS (HUMAN).
Q15478 SODIUM CHANNEL ALPHA SUBUNIT - HOMO SAPIENS (HUMAN).
Q15858 SODIUM CHANNEL ALPHA SUBUNIT - HOMO SAPIENS (HUMAN).
Q17314 SODIUM CHANNEL - CYANEA CAPILLATA.
Q24528 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q24529 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q24530 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q24531 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q24532 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q25150 VOLTAGE-GATED SODIUM CHANNEL - HALOCYNTHIA RORETZI (SEA SQUIRT).
Q25377 SODIUM CHANNEL - LOLIGO OPALESCENS (CALIFORNIA MARKET SQUID).
Q25439 VOLTAGE-SENSITIVE SODIUM CHANNEL - MUSCA DOMESTICA (HOUSE FLY).
Q25440 VOLTAGE-SENSITIVE SODIUM CHANNEL - MUSCA DOMESTICA (HOUSE FLY).
Q28371 SKELETAL MUSCLE SODIUM CHANNEL ALPHA-SUBUNIT - Equus caballus (Horse).
Q28644 SODIUM CHANNEL ALPHA-SUBUNIT - ORYCTOLAGUS CUNICULUS (RABBIT).
Q60858 SODIUM CHANNEL, VOLTAGE-GATED, TYPE VIII, ALPHA POLYPEPTIDE (SCN8A) - Mus musculus (Mouse).
Q62205 SODIUM CHANNEL 25 - MUS MUSCULUS (MOUSE).
Q62243 SODIUM CHANNEL - MUS MUSCULUS (MOUSE).
Q62467 SODIUM CHANNEL, VOLTAGE-GATED, TYPE VI, ALPHA POLYPEPTIDE (VOLTAGE-GATED SODIUM CHANNEL PROTEIN) - MUS MUSCULUS (MOUSE).
Q62968 SODIUM CHANNEL PN3 - RATTUS NORVEGICUS (RAT).
Q63541 SODIUM CHANNEL PROTEIN 6 - Rattus norvegicus (Rat).
Q63554 VOLATAGE-GATED SODIUM CHANNEL - RATTUS NORVEGICUS (RAT).
Q94615 VOLTAGE-SENSITIVE SODIUM CHANNEL - MUSCA DOMESTICA (HOUSE FLY).
Q9YGN7 VOLTAGE-DEPENDENT SODIUM CHANNEL - CYNOPS PYRRHOGASTER (JAPANESE COMMON NEWT).
Scan History
SPTR37_10f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
SYIIISFLVVVNMYIAVILE CIN1_RAT 1768 1768 -
SYIIISFLVVVNMYIAVILE CIN2_RAT 1758 1758 -
SYIIISFLVVVNMYIAVILE CIN3_RAT 1704 1704 -
SYIIISFLVVVNMYIAVILE Q15858 1731 1731 -
SYIIISFLVVVNMYIAVILE Q9YGN7 1760 1760 -
SYIIISFLIVVNMYIAIILE CIN4_HUMAN 1580 1580 -
SYIIISFLIVVNMYIAIILE Q15478 1580 1580 -
SYIIISFLIVVNMYIAIILE O70611 1573 1573 -
SYIIISFLIVVNMYIAIILE CIN4_RAT 1573 1573 -
TYIIISFLIVVNMYIAVILE O46669 1711 1711 -
TYIIISFLIVVNMYIAVILE P70276 1705 1705 -
TYIIISFLIVVNMYIAVILE Q62968 1705 1705 -
TYIIISFLIVVNMYIAVILE Q63554 1706 1706 -
TYIIISFLIVVNMYIAIILE CIN5_HUMAN 1754 1754 -
TYIIISFLIVVNMYIAIILE CIN5_RAT 1756 1756 -
SYIIISFLVVLNMYIAVILE Q14472 1758 1758 -
SYIIISFLIVVNMYIAIILE O88420 1746 1746 -
SYIIISFLIVVNMYIAIILE Q60858 1500 1500 -
SYIIISFLIVVNMCIAIILE Q63541 1744 1744 -
TYLVISFLVVINMYIAVILE Q25377 1571 1571 -
SYLVISFLIVINMYIAVILE CINA_DROME 1842 1842 -
SYLVISFLIVINMYIAVILE Q94615 1830 1830 -
SYLVISFLIVINMYIAVILE Q25439 1830 1830 -
SYLVISFLIVINMYIAVILE Q24528 1788 1788 -
SYLVISFLIVINMYIAVILE O01306 1811 1811 -
TYLIMTFLIVVNMYIAIILE Q25150 1821 1821 -
TYLVVSFLVVVNMYIAVILE P90670 1714 1714 -
SYIILSFLVVVNMYIAIILE CINA_ELEEL 1549 1549 -
SYIIIVFMIVFNMYIAVILE CIN1_LOLBL 1333 1333 -
SYLIINAFVIVNMYIAVILE O02037 1526 1526 -
TFILFTFLIIINMYIAIILE O44930 1590 1590 -
SYIALIVLIMINMYIAVILE Q17314 1507 1507 -
SYILISWLIIVNMYIVVVME CIN6_HUMAN 1478 1478 -
SYILISWLIIVNMYVVLIME P97706 1499 1499 -

Motif 2 width=14
Element Seqn Id St Int Rpt
DDFEMFYEVWEKFD CIN1_RAT 1803 15 -
DDFEMFYEVWEKFD CIN2_RAT 1793 15 -
DDFEMFYEVWEKFD CIN3_RAT 1739 15 -
DDFEMFYEVWEKFD Q15858 1766 15 -
DDFEMFYEVWEKFD Q9YGN7 1795 15 -
DDFEMFYETWEKFD CIN4_HUMAN 1615 15 -
DDFEMFYETWEKFD Q15478 1615 15 -
DDFEMFYETWEKFD O70611 1608 15 -
DDFEMFYETWEKFD CIN4_RAT 1608 15 -
DDFDMFYETWEKFD O46669 1746 15 -
DDFDMFYETWEKFD P70276 1740 15 -
DDFDMFYETWEKFD Q62968 1740 15 -
DDFDMFYETWEKFD Q63554 1741 15 -
DDFDMFYEIWEKFD CIN5_HUMAN 1789 15 -
DDFDMFYEIWEKFD CIN5_RAT 1791 15 -
DDFEMFYEVWEKFD Q14472 1793 15 -
DDFETFYEIWEKFD O88420 1781 15 -
DDFETFYEIWEKFD Q60858 1535 15 -
DDFETFYEIWEKFD Q63541 1779 15 -
DDFDMYYEKWEKFD Q25377 1606 15 -
DDYDMYYEIWQQFD CINA_DROME 1877 15 -
DDYDMYYEIWQQFD Q94615 1865 15 -
DDYDMYYEIWQQFD Q25439 1865 15 -
DDYDMYYEIWQQFD Q24528 1823 15 -
DDYDMYYEIWQQFD O01306 1846 15 -
DDFEMFYEIWERFD Q25150 1856 15 -
DDFDMYYEKWEKYD P90670 1749 15 -
DDFVMFDETWHKFD CINA_ELEEL 1584 15 -
DDLDMFYGVWEQYD CIN1_LOLBL 1368 15 -
DDYDLFYEVWEKYD O02037 1561 15 -
DDLDMFYYHWERFD O44930 1625 15 -
DDLEAYYSVWEQFD Q17314 1542 15 -
DDFRKFFQVWKRFD CIN6_HUMAN 1513 15 -
DDFRRFFKVWNRFD P97706 1534 15 -
Final Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
SYIIISFLVVVNMYIAVILE CIN1_RAT 1768 1768 -
SYIIISFLVVVNMYIAVILE CIN2_RAT 1758 1758 -
SYIIISFLVVVNMYIAVILE CIN3_RAT 1704 1704 -
SYIIISFLVVVNMYIAVILE Q15858 1731 1731 -
SYIIISFLVVVNMYIAVILE Q28644 1739 1739 -
SYIIISFLVVVNMYIAVILE Q62205 65 65 -
SYIIISFLVVVNMYIAVILE Q9YGN7 1760 1760 -
SYIIISFLIVVNMYIAIILE CIN4_HUMAN 1580 1580 -
SYIIISFLIVVNMYIAIILE Q15478 1580 1580 -
SYIIISFLIVVNMYIAIILE O70611 1573 1573 -
SYIIISFLIVVNMYIAIILE CIN4_RAT 1573 1573 -
TYIIISFLIVVNMYIAVILE O46669 1711 1711 -
TYIIISFLIVVNMYIAVILE P70276 1705 1705 -
TYIIISFLIVVNMYIAVILE Q62243 270 270 -
TYIIISFLIVVNMYIAVILE Q62968 1705 1705 -
TYIIISFLIVVNMYIAVILE Q63554 1706 1706 -
TYIIISFLIVVNMYIAIILE CIN5_HUMAN 1754 1754 -
TYIIISFLIVVNMYIAIILE CIN5_RAT 1756 1756 -
SYIIISFLIVVNMYIAVILE O88457 1566 1566 -
SYIIISFLVVLNMYIAVILE Q14472 1758 1758 -
SYIIISFLIVVNMYIAIILE O88420 1746 1746 -
SYIIISFLIVVNMYIAIILE Q60858 1500 1500 -
SYIIISFLIVVNMYIAIILE O95788 1748 1748 -
SYIIISFLIVVNMYIAIILE O88421 1756 1756 -
SYIIISFLIVVNMCIAIILE Q63541 1744 1744 -
TYLVISFLVVINMYIAVILE Q25377 1571 1571 -
SYLVISFLIVINMYIAVILE CINA_DROME 1842 1842 -
SYLVISFLIVINMYIAVILE Q94615 1830 1830 -
SYLVISFLIVINMYIAVILE Q25440 1830 1830 -
SYLVISFLIVINMYIAVILE Q25439 1830 1830 -
SYLVISFLIVINMYIAVILE Q24532 1821 1821 -
SYLVISFLIVINMYIAVILE Q24531 1829 1829 -
SYLVISFLIVINMYIAVILE Q24530 1834 1834 -
SYLVISFLIVINMYIAVILE Q24529 1832 1832 -
SYLVISFLIVINMYIAVILE Q24528 1788 1788 -
SYLVISFLIVINMYIAVILE O01307 1811 1811 -
SYLVISFLIVINMYIAVILE O01306 1811 1811 -
TYLIMTFLIVVNMYIAIILE Q25150 1821 1821 -
SYIIISFLIVVNMYIAIILE Q28371 1577 1577 -
TYLVVSFLVVVNMYIAVILE P90670 1714 1714 -
SYIILSFLVVVNMYIAIILE CINA_ELEEL 1549 1549 -
SYIIIVFMIVFNMYIAVILE CIN1_LOLBL 1333 1333 -
SYLIINAFVIVNMYIAVILE O02037 1526 1526 -
TFILFTFLIIINMYIAIILE O44930 1590 1590 -
SYIALIVLIMINMYIAVILE Q17314 1507 1507 -
SYIILIVLIIINMYIAVILE O62604 1452 1452 -
SYILISWLIIVNMYIVLIME Q62467 1478 1478 -
SYILISWLIIVNMYIVVVME CIN6_HUMAN 1478 1478 -
SYILISWLIIVNMYVVLIME P97706 1499 1499 -

Motif 2 width=14
Element Seqn Id St Int Rpt
DDFEMFYEVWEKFD CIN1_RAT 1803 15 -
DDFEMFYEVWEKFD CIN2_RAT 1793 15 -
DDFEMFYEVWEKFD CIN3_RAT 1739 15 -
DDFEMFYEVWEKFD Q15858 1766 15 -
DDFEMFYEVWEKFD Q28644 1774 15 -
DDFEMFYEVWEKFD Q62205 100 15 -
DDFEMFYEVWEKFD Q9YGN7 1795 15 -
DDFEMFYETWEKFD CIN4_HUMAN 1615 15 -
DDFEMFYETWEKFD Q15478 1615 15 -
DDFEMFYETWEKFD O70611 1608 15 -
DDFEMFYETWEKFD CIN4_RAT 1608 15 -
DDFDMFYETWEKFD O46669 1746 15 -
DDFDMFYETWEKFD P70276 1740 15 -
DDFDMFYETWEKFD Q62243 305 15 -
DDFDMFYETWEKFD Q62968 1740 15 -
DDFDMFYETWEKFD Q63554 1741 15 -
DDFDMFYEIWEKFD CIN5_HUMAN 1789 15 -
DDFDMFYEIWEKFD CIN5_RAT 1791 15 -
DDFEIFYEVWEKFD O88457 1601 15 -
DDFEMFYEVWEKFD Q14472 1793 15 -
DDFETFYEIWEKFD O88420 1781 15 -
DDFETFYEIWEKFD Q60858 1535 15 -
DDFETFYEIWEKFD O95788 1783 15 -
DDFETFYEIWEKFD O88421 1791 15 -
DDFETFYEIWEKFD Q63541 1779 15 -
DDFDMYYEKWEKFD Q25377 1606 15 -
DDYDMYYEIWQQFD CINA_DROME 1877 15 -
DDYDMYYEIWQQFD Q94615 1865 15 -
DDYDMYYEIWQQFD Q25440 1865 15 -
DDYDMYYEIWQQFD Q25439 1865 15 -
DDYDMYYEIWQQFD Q24532 1856 15 -
DDYDMYYEIWQQFD Q24531 1864 15 -
DDYDMYYEIWQQFD Q24530 1869 15 -
DDYDMYYEIWQQFD Q24529 1867 15 -
DDYDMYYEIWQQFD Q24528 1823 15 -
DDYDMYYEIWQQFD O01307 1846 15 -
DDYDMYYEIWQQFD O01306 1846 15 -
DDFEMFYEIWERFD Q25150 1856 15 -
DDFEIFFEKWEKFG Q28371 1612 15 -
DDFDMYYEKWEKYD P90670 1749 15 -
DDFVMFDETWHKFD CINA_ELEEL 1584 15 -
DDLDMFYGVWEQYD CIN1_LOLBL 1368 15 -
DDYDLFYEVWEKYD O02037 1561 15 -
DDLDMFYYHWERFD O44930 1625 15 -
DDLEAYYSVWEQFD Q17314 1542 15 -
DDLEAYYTVWEDYD O62604 1487 15 -
DDFRRFFRVWNRFD Q62467 1513 15 -
DDFRKFFQVWKRFD CIN6_HUMAN 1513 15 -
DDFRRFFKVWNRFD P97706 1534 15 -