WORKLIST ENTRIES (1):
NACHANNEL View alignment Voltage-gated Na+ channel alpha subunit signature
Type of fingerprint: COMPOUND with 2 elements
Links:
PRINTS; PR00169 KCHANNEL; PR00167 CACHANNEL; PR00168 ISKCHANNEL
PRINTS; PR01664 NACHANNEL1; PR01665 NACHANNEL4; PR01666 NACHANNEL5
PRINTS; PR01667 NACHANNEL8
INTERPRO; IPR001696
Creation date 06-MAY-1993; UPDATE 22-MAY-2000
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).
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 channel 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 FINGERPRINT INDEX
2| 49 49
--+-----------
| 1 2
True positives..
Q9YGN7 Q62205 Q28644 Q15858
CIN3_RAT CIN2_RAT CIN1_RAT CIN4_HUMAN
Q15478 O70611 CIN4_RAT O46669
P70276 Q62243 Q62968 Q63554
CIN5_HUMAN CIN5_RAT O88457 Q14472
O88420 Q60858 O95788 O88421
Q63541 Q25377 CINA_DROME Q94615
Q25440 Q25439 Q24532 Q24531
Q24530 Q24529 Q24528 O01307
O01306 Q25150 Q28371 P90670
CINA_ELEEL CIN1_LOLBL O02037 O44930
Q17314 O62604 Q62467 CIN6_HUMAN
P97706
PROTEIN TITLES
Q9YGN7 VOLTAGE-DEPENDENT SODIUM CHANNEL - CYNOPS PYRRHOGASTER (JAPA
Q62205 SODIUM CHANNEL 25 - MUS MUSCULUS (MOUSE).
Q28644 SODIUM CHANNEL ALPHA-SUBUNIT - ORYCTOLAGUS CUNICULUS (RABBIT
Q15858 SODIUM CHANNEL ALPHA SUBUNIT - HOMO SAPIENS (HUMAN).
CIN3_RAT SODIUM CHANNEL PROTEIN, BRAIN III ALPHA SUBUNIT - RATTUS NOR
CIN2_RAT SODIUM CHANNEL PROTEIN, BRAIN II ALPHA SUBUNIT - RATTUS NORV
CIN1_RAT SODIUM CHANNEL PROTEIN, BRAIN I ALPHA SUBUNIT - RATTUS NORVE
CIN4_HUMAN SODIUM CHANNEL PROTEIN, SKELETAL MUSCLE ALPHA-SUBUNIT - HOMO
Q15478 SODIUM CHANNEL ALPHA SUBUNIT - HOMO SAPIENS (HUMAN).
O70611 RAT SKELETAL MUSCLE TYPE 1 VOLTAGE-GATED SODIUM CHANNEL (RSK
CIN4_RAT SODIUM CHANNEL PROTEIN, SKELETAL MUSCLE ALPHA-SUBUNIT (MU-1)
O46669 TTX-RESISTANT SODIUM CHANNEL - CANIS FAMILIARIS (DOG).
P70276 SODIUM CHANNEL, TYPE X, ALPHA POLYPEPTIDE (VOLTAGE-GATED SOD
Q62243 SODIUM CHANNEL - MUS MUSCULUS (MOUSE).
Q62968 SODIUM CHANNEL PN3 - RATTUS NORVEGICUS (RAT).
Q63554 VOLATAGE-GATED SODIUM CHANNEL - RATTUS NORVEGICUS (RAT).
CIN5_HUMAN SODIUM CHANNEL PROTEIN, CARDIAC MUSCLE ALPHA-SUBUNIT (HH1) -
CIN5_RAT SODIUM CHANNEL PROTEIN, CARDIAC MUSCLE ALPHA-SUBUNIT - RATTU
O88457 VOLTAGE-GATED NA CHANNEL ALPHA SUBUNIT NAN - RATTUS NORVEGIC
Q14472 VOLTAGE-GATED SODIUM CHANNEL (VOLTAGE-GATED SODIUM CHANNEL S
O88420 VOLTAGE-GATED SODIUM CHANNEL RPN4 - RATTUS NORVEGICUS (RAT).
Q60858 SODIUM CHANNEL, VOLTAGE-GATED, TYPE VIII, ALPHA POLYPEPTIDE
O95788 VOLTAGE-GATED SODIUM CHANNEL ALPHA SUBUNIT - HOMO SAPIENS (H
O88421 VOLTAGE-GATED SODIUM CHANNEL VARIANT RPN4A - RATTUS NORVEGIC
Q63541 SODIUM CHANNEL PROTEIN 6 - RATTUS NORVEGICUS (RAT).
Q25377 SODIUM CHANNEL - LOLIGO OPALESCENS (CALIFORNIA MARKET SQUID)
CINA_DROME SODIUM CHANNEL PROTEIN PARA (PARALYTIC PROTEIN) - DROSOPHILA
Q94615 VOLTAGE-SENSITIVE SODIUM CHANNEL - MUSCA DOMESTICA (HOUSE FL
Q25440 VOLTAGE-SENSITIVE SODIUM CHANNEL - MUSCA DOMESTICA (HOUSE FL
Q25439 VOLTAGE-SENSITIVE SODIUM CHANNEL - MUSCA DOMESTICA (HOUSE FL
Q24532 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUI
Q24531 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUI
Q24530 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUI
Q24529 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUI
Q24528 SODIUM CHANNEL ALPHA SUBUNIT - DROSOPHILA MELANOGASTER (FRUI
O01307 PARA SODIUM CHANNEL - BLATTELLA GERMANICA (GERMAN COCKROACH)
O01306 PARA SODIUM CHANNEL - BLATTELLA GERMANICA (GERMAN COCKROACH)
Q25150 VOLTAGE-GATED SODIUM CHANNEL - HALOCYNTHIA RORETZI (SEA SQUI
Q28371 SKELETAL MUSCLE SODIUM CHANNEL ALPHA-SUBUNIT - EQUUS CABALLU
P90670 SODIUM CHANNEL ALPHA-SUBUNIT SCAP1 - APLYSIA CALIFORNICA (CA
CINA_ELEEL SODIUM CHANNEL PROTEIN (NA+ CHANNEL) - ELECTROPHORUS ELECTRI
CIN1_LOLBL SODIUM CHANNEL PROTEIN I, BRAIN - LOLIGO BLEEKERI (BLEEKER'S
O02037 VOLTAGE-GATED SODIUM CHANNEL HOMOLOG BDNA1 - BDELLOURA CANDI
O44930 PUTATIVE VOLTAGE-GATED SODIUM CHANNEL - AIPTASIA PALLIDA.
Q17314 SODIUM CHANNEL - CYANEA CAPILLATA.
O62604 VOLTAGE-GATED SODIUM CHANNEL ALPHA SUBUNIT - POLYORCHIS PENI
Q62467 SODIUM CHANNEL, VOLTAGE-GATED, TYPE VI, ALPHA POLYPEPTIDE (V
CIN6_HUMAN SODIUM CHANNEL PROTEIN, CARDIAC AND SKELETAL MUSCLE ALPHA-SU
P97706 SODIUM CHANNEL - RATTUS NORVEGICUS (RAT).
SCAN HISTORY
SPTR37_10f 2 100 NSINGLE
INITIAL MOTIF SETS
NACHANNEL1 Length of motif = 20 Motif number = 1
Voltage-gated Na+ channel alpha subunit motif I - 1
PCODE ST INT
SYIIISFLVVLNMYIAVILE Q14472 1758 1758
SYIIISFLVVVNMYIAVILE CIN2_RAT 1758 1758
SYIIISFLVVVNMYIAVILE CIN1_RAT 1768 1768
SYIIISFLVVVNMYIAVILE CIN3_RAT 1704 1704
SYIIISFLVVVNMYIAVILE Q9YGN7 1760 1760
SYIIISFLIVVNMYIAIILE O88420 1746 1746
SYIIISFLIVVNMYIAIILE Q60858 1500 1500
SYIIISFLIVVNMCIAIILE Q63541 1744 1744
SYIIISFLVVVNMYIAVILE Q15858 1731 1731
TYIIISFLIVVNMYIAIILE CIN5_HUMAN 1754 1754
TYIIISFLIVVNMYIAIILE CIN5_RAT 1756 1756
TYIIISFLIVVNMYIAVILE Q62968 1705 1705
TYIIISFLIVVNMYIAVILE Q63554 1706 1706
TYIIISFLIVVNMYIAVILE P70276 1705 1705
TYIIISFLIVVNMYIAVILE O46669 1711 1711
SYIIISFLIVVNMYIAIILE O70611 1573 1573
SYIIISFLIVVNMYIAIILE CIN4_RAT 1573 1573
SYIIISFLIVVNMYIAIILE Q15478 1580 1580
SYIIISFLIVVNMYIAIILE CIN4_HUMAN 1580 1580
TYLVISFLVVINMYIAVILE Q25377 1571 1571
TYLIMTFLIVVNMYIAIILE Q25150 1821 1821
SYLVISFLIVINMYIAVILE Q94615 1830 1830
SYLVISFLIVINMYIAVILE Q25439 1830 1830
SYLVISFLIVINMYIAVILE CINA_DROME 1842 1842
SYLVISFLIVINMYIAVILE Q24528 1788 1788
SYLVISFLIVINMYIAVILE O01306 1811 1811
SYIILSFLVVVNMYIAIILE CINA_ELEEL 1549 1549
SYLIINAFVIVNMYIAVILE O02037 1526 1526
SYILISWLIIVNMYIVVVME CIN6_HUMAN 1478 1478
TYLVVSFLVVVNMYIAVILE P90670 1714 1714
SYIIIVFMIVFNMYIAVILE CIN1_LOLBL 1333 1333
SYILISWLIIVNMYVVLIME P97706 1499 1499
SYIALIVLIMINMYIAVILE Q17314 1507 1507
TFILFTFLIIINMYIAIILE O44930 1590 1590
NACHANNEL2 Length of motif = 14 Motif number = 2
Voltage-gated Na+ channel alpha subunit motif II - 1
PCODE ST INT
DDFEMFYEVWEKFD Q14472 1793 15
DDFEMFYEVWEKFD CIN2_RAT 1793 15
DDFEMFYEVWEKFD CIN1_RAT 1803 15
DDFEMFYEVWEKFD CIN3_RAT 1739 15
DDFEMFYEVWEKFD Q9YGN7 1795 15
DDFETFYEIWEKFD O88420 1781 15
DDFETFYEIWEKFD Q60858 1535 15
DDFETFYEIWEKFD Q63541 1779 15
DDFEMFYEVWEKFD Q15858 1766 15
DDFDMFYEIWEKFD CIN5_HUMAN 1789 15
DDFDMFYEIWEKFD CIN5_RAT 1791 15
DDFDMFYETWEKFD Q62968 1740 15
DDFDMFYETWEKFD Q63554 1741 15
DDFDMFYETWEKFD P70276 1740 15
DDFDMFYETWEKFD O46669 1746 15
DDFEMFYETWEKFD O70611 1608 15
DDFEMFYETWEKFD CIN4_RAT 1608 15
DDFEMFYETWEKFD Q15478 1615 15
DDFEMFYETWEKFD CIN4_HUMAN 1615 15
DDFDMYYEKWEKFD Q25377 1606 15
DDFEMFYEIWERFD Q25150 1856 15
DDYDMYYEIWQQFD Q94615 1865 15
DDYDMYYEIWQQFD Q25439 1865 15
DDYDMYYEIWQQFD CINA_DROME 1877 15
DDYDMYYEIWQQFD Q24528 1823 15
DDYDMYYEIWQQFD O01306 1846 15
DDFVMFDETWHKFD CINA_ELEEL 1584 15
DDYDLFYEVWEKYD O02037 1561 15
DDFRKFFQVWKRFD CIN6_HUMAN 1513 15
DDFDMYYEKWEKYD P90670 1749 15
DDLDMFYGVWEQYD CIN1_LOLBL 1368 15
DDFRRFFKVWNRFD P97706 1534 15
DDLEAYYSVWEQFD Q17314 1542 15
DDLDMFYYHWERFD O44930 1625 15
FINAL MOTIF SETS
NACHANNEL1 Length of motif = 20 Motif number = 1
Voltage-gated Na+ channel alpha subunit motif I - 2
PCODE ST INT
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
NACHANNEL2 Length of motif = 14 Motif number = 2
Voltage-gated Na+ channel alpha subunit motif II - 2
PCODE ST INT
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
User query: Display/Full Code "NACHANNEL"