BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy14955
(191 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RVY|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Ile217cys, 2.7 A)
pdb|3RVY|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Ile217cys, 2.7 A)
pdb|3RVZ|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Ile217cys, 2.8 A)
pdb|3RVZ|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Ile217cys, 2.8 A)
Length = 285
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 39/142 (27%), Positives = 67/142 (47%), Gaps = 8/142 (5%)
Query: 41 LFSLFIITTILTNCILMIMPGTPTIESTEVIFTGIYTFESAVKVMARGFILESF----TY 96
F+ FII I+ N I M + + T + ++T ++ + + + IL + ++
Sbjct: 31 FFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFN-QIVITIFTIEIILRIYVHRISF 89
Query: 97 LRDAWNWLDFIVIALAYVTMGIDLGNLAALRTFRVLRALKTVAIVPGLKTIVGAVIESVK 156
+D W+ DF V+A++ V LR RVLR + V VP ++ IV A+I +
Sbjct: 90 FKDPWSLFDFFVVAISLVPTS---SGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIP 146
Query: 157 NLRDVIILTMFSLSVFALMGLQ 178
+ VI L +FA+M Q
Sbjct: 147 GMLSVIALMTLFFYIFAIMATQ 168
>pdb|4DXW|A Chain A, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
pdb|4DXW|B Chain B, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
pdb|4DXW|C Chain C, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
pdb|4DXW|D Chain D, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
Length = 229
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 71/143 (49%), Gaps = 11/143 (7%)
Query: 41 LFSLFIITTILTNCILMIMPGTPTIESTEVIFTGIYTFESAVKVMARGFILESFT----- 95
+F +++ I+ N +L+ G T E + I+ + + + IL F
Sbjct: 13 IFQFTVVSIIILNAVLI---GATTYELDPLFLETIHLLDYGITIFFVIEILIRFIGEKQK 69
Query: 96 --YLRDAWNWLDFIVIALAYVTMGIDLGNLAALRTFRVLRALKTVAIVPGLKTIVGAVIE 153
+ + WN D +++A++ + + + + LR R+ R L+ ++++P LK I+ A++E
Sbjct: 70 ADFFKSGWNIFDTVIVAISLIPIP-NNSSFLVLRLLRIFRVLRLISVIPELKQIIEAILE 128
Query: 154 SVKNLRDVIILTMFSLSVFALMG 176
SV+ + V +L L ++A MG
Sbjct: 129 SVRRVFFVSLLLFIILYIYATMG 151
>pdb|4EKW|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
pdb|4EKW|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
pdb|4EKW|C Chain C, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
pdb|4EKW|D Chain D, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
Length = 285
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 63/142 (44%), Gaps = 8/142 (5%)
Query: 41 LFSLFIITTILTNCILMIMPGTPTIESTEVIFTGIYTFESAVKVMARGFILESF----TY 96
F+ FII I+ N I + + T + ++T ++ + + + IL + ++
Sbjct: 31 FFTKFIIYLIVLNGITXGLETSKTFXQSFGVYTTLFN-QIVITIFTIEIILRIYVHRISF 89
Query: 97 LRDAWNWLDFIVIALAYVTMGIDLGNLAALRTFRVLRALKTVAIVPGLKTIVGAVIESVK 156
+D W+ DF V+A++ V LR RVLR + V VP + IV A+I +
Sbjct: 90 FKDPWSLFDFFVVAISLVPTS---SGFEILRVLRVLRLFRLVTAVPQXRKIVSALISVIP 146
Query: 157 NLRDVIILTMFSLSVFALMGLQ 178
VI L +FA+ Q
Sbjct: 147 GXLSVIALXTLFFYIFAIXATQ 168
>pdb|3RW0|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Met221cys, 2.95 A)
pdb|3RW0|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Met221cys, 2.95 A)
Length = 285
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 63/142 (44%), Gaps = 8/142 (5%)
Query: 41 LFSLFIITTILTNCILMIMPGTPTIESTEVIFTGIYTFESAVKVMARGFILESF----TY 96
F+ FII I+ N I + + T + ++T ++ + + + IL + ++
Sbjct: 31 FFTKFIIYLIVLNGITXGLETSKTFXQSFGVYTTLFN-QIVITIFTIEIILRIYVHRISF 89
Query: 97 LRDAWNWLDFIVIALAYVTMGIDLGNLAALRTFRVLRALKTVAIVPGLKTIVGAVIESVK 156
+D W+ DF V+A++ V LR RVLR + V VP + IV A+I +
Sbjct: 90 FKDPWSLFDFFVVAISLVPTS---SGFEILRVLRVLRLFRLVTAVPQXRKIVSALISVIP 146
Query: 157 NLRDVIILTMFSLSVFALMGLQ 178
VI L +FA+ Q
Sbjct: 147 GXLSVIALXTLFFYIFAIXATQ 168
>pdb|1QG9|A Chain A, Second Repeat (Is2mic) From Voltage-Gated Sodium Channel
Length = 21
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 67 STEVIFTGIYTFESAVKVMAR 87
+ E FTGIYTFES +K++AR
Sbjct: 1 NVEYTFTGIYTFESLIKILAR 21
>pdb|2LCM|A Chain A, Nmr Structure Of S3-4 Peptide
Length = 28
Score = 30.4 bits (67), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 119 DLGNLAALRTFRVLRALKTVAIVPGLK 145
D+ + +LR RVLR LKT+ +P LK
Sbjct: 2 DINTIKSLRVLRVLRPLKTIKRLPKLK 28
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.329 0.142 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,799,656
Number of Sequences: 62578
Number of extensions: 165020
Number of successful extensions: 352
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 345
Number of HSP's gapped (non-prelim): 7
length of query: 191
length of database: 14,973,337
effective HSP length: 93
effective length of query: 98
effective length of database: 9,153,583
effective search space: 897051134
effective search space used: 897051134
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)