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= psy13561
         (99 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>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 = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 6/92 (6%)

Query: 6   DYFQCGWNIFDLIVVTASLVDLMTE----FVDGLSVLRGLRL--SWTTMKVLLSIIISTI 59
           D+F+ GWNIFD ++V  SL+ +        +  L + R LRL      +K ++  I+ ++
Sbjct: 71  DFFKSGWNIFDTVIVAISLIPIPNNSSFLVLRLLRIFRVLRLISVIPELKQIIEAILESV 130

Query: 60  GALGNLTFVLVIVIYIFAVIGMQLFSKDYTSE 91
             +  ++ +L I++YI+A +G  LF  D  S 
Sbjct: 131 RRVFFVSLLLFIILYIYATMGAILFGNDDPSR 162


>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 = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 50/88 (56%), Gaps = 6/88 (6%)

Query: 6   DYFQCGWNIFDLIVVTASLVDLMTEFVDGLSVLRGLRL-----SWTTMKVLLSIIISTIG 60
            +F+  W++FD  VV  SLV   + F + L VLR LRL     +   M+ ++S +IS I 
Sbjct: 88  SFFKDPWSLFDFFVVAISLVPTSSGF-EILRVLRVLRLFRLVTAVPQMRKIVSALISVIP 146

Query: 61  ALGNLTFVLVIVIYIFAVIGMQLFSKDY 88
            + ++  ++ +  YIFA++  QLF + +
Sbjct: 147 GMLSVIALMTLFFYIFAIMATQLFGERF 174


>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 = 38.5 bits (88), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 6/88 (6%)

Query: 6   DYFQCGWNIFDLIVVTASLVDLMTEFVDGLSVLRGLRL-----SWTTMKVLLSIIISTIG 60
            +F+  W++FD  VV  SLV   + F + L VLR LRL     +    + ++S +IS I 
Sbjct: 88  SFFKDPWSLFDFFVVAISLVPTSSGF-EILRVLRVLRLFRLVTAVPQXRKIVSALISVIP 146

Query: 61  ALGNLTFVLVIVIYIFAVIGMQLFSKDY 88
              ++  +  +  YIFA+   QLF + +
Sbjct: 147 GXLSVIALXTLFFYIFAIXATQLFGERF 174


>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 = 38.5 bits (88), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 6/88 (6%)

Query: 6   DYFQCGWNIFDLIVVTASLVDLMTEFVDGLSVLRGLRL-----SWTTMKVLLSIIISTIG 60
            +F+  W++FD  VV  SLV   + F + L VLR LRL     +    + ++S +IS I 
Sbjct: 88  SFFKDPWSLFDFFVVAISLVPTSSGF-EILRVLRVLRLFRLVTAVPQXRKIVSALISVIP 146

Query: 61  ALGNLTFVLVIVIYIFAVIGMQLFSKDY 88
              ++  +  +  YIFA+   QLF + +
Sbjct: 147 GXLSVIALXTLFFYIFAIXATQLFGERF 174


  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    0.143    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,459,690
Number of Sequences: 62578
Number of extensions: 65915
Number of successful extensions: 117
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 111
Number of HSP's gapped (non-prelim): 4
length of query: 99
length of database: 14,973,337
effective HSP length: 65
effective length of query: 34
effective length of database: 10,905,767
effective search space: 370796078
effective search space used: 370796078
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: 45 (21.9 bits)