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= 004951
         (722 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 = 32.7 bits (73), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 38/198 (19%), Positives = 80/198 (40%), Gaps = 35/198 (17%)

Query: 181 DFLVYGLYLSPIAFNFLPLRIAPYIRVVFFILNIRQLRDTLFVLAGMLGTYLNVLGNMV- 239
           DF V  + L P +  F  LR+   +R+   +  + Q+R  +  L  ++   L+V+  M  
Sbjct: 98  DFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTL 157

Query: 240 --------------------FTSFGTTLYQMFVLFTTSN-NPDVWIPAYKASRWYCLFFV 278
                               F + G + Y +F + T  + +  +  P  +   +  +FF+
Sbjct: 158 FFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFI 217

Query: 279 LYVLIGVYFVTNLILAVVYDSFKSQLAKQVSEMDRMRRRTLGKAFNLIDNYNVGFLNKEQ 338
            ++ +  + + NL++A+  D+      K+        +  + +  +  DN N       +
Sbjct: 218 PFIFVVTFVMINLVVAICVDAMAILNQKE-------EQHIIDEVQSHEDNIN------NE 264

Query: 339 CIKLFEELNKYRTLPNIS 356
            IKL EE+ + + L   S
Sbjct: 265 IIKLREEIVELKELIKTS 282


>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 = 29.3 bits (64), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 38/199 (19%), Positives = 78/199 (39%), Gaps = 37/199 (18%)

Query: 181 DFLVYGLYLSPIAFNFLPLRIAPYIRVVFFILNIRQLRDTLFVLAGMLGTYLNVLGNMV- 239
           DF V  + L P +  F  LR+   +R+   +  + Q R  +  L  ++   L+V+     
Sbjct: 98  DFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQXRKIVSALISVIPGXLSVIALXTL 157

Query: 240 --------------------FTSFGTTLYQMFVLFTTSN-NPDVWIPAYKASRWYCLFFV 278
                               F + G + Y +F + T  + +  +  P  +   +  +FF+
Sbjct: 158 FFYIFAIXATQLFGERFPEWFGTLGESFYTLFQVXTLESWSXGIVRPLXEVYPYAWVFFI 217

Query: 279 LYVLIGVYFVTNLILAVVYDSFKSQLAKQVSE-MDRMRRRTLGKAFNLIDNYNVGFLNKE 337
            ++ +  +   NL++A++ D+      K+    +D ++           DN N       
Sbjct: 218 PFIFVVTFVXINLVVAIIVDAXAILNQKEEQHIIDEVQSHE--------DNIN------N 263

Query: 338 QCIKLFEELNKYRTLPNIS 356
           + IKL EE+ + + L   S
Sbjct: 264 EIIKLREEIVELKELIKTS 282


>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 = 28.9 bits (63), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 26/141 (18%), Positives = 58/141 (41%), Gaps = 22/141 (15%)

Query: 181 DFLVYGLYLSPIAFNFLPLRIAPYIRVVFFILNIRQLRDTLFVLAGMLGTYLNVLGNMV- 239
           DF V  + L P +  F  LR+   +R+   +  + Q R  +  L  ++   L+V+     
Sbjct: 98  DFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQXRKIVSALISVIPGXLSVIALXTL 157

Query: 240 --------------------FTSFGTTLYQMFVLFTTSN-NPDVWIPAYKASRWYCLFFV 278
                               F + G + Y +F + T  + +  +  P  +   +  +FF+
Sbjct: 158 FFYIFAIXATQLFGERFPEWFGTLGESFYTLFQVXTLESWSXGIVRPLXEVYPYAWVFFI 217

Query: 279 LYVLIGVYFVTNLILAVVYDS 299
            ++ +  +   NL++A++ D+
Sbjct: 218 PFIFVVTFVXINLVVAIIVDA 238


  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
   0.326    0.141    0.442 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,015,810
Number of Sequences: 62578
Number of extensions: 681286
Number of successful extensions: 1756
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1750
Number of HSP's gapped (non-prelim): 7
length of query: 722
length of database: 14,973,337
effective HSP length: 106
effective length of query: 616
effective length of database: 8,340,069
effective search space: 5137482504
effective search space used: 5137482504
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.8 bits)