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= psy1892
         (64 letters)

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

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



>pdb|1EJP|A Chain A, Solution Structure Of The Syndecan-4 Whole Cytoplasmic
          Domain
 pdb|1EJP|B Chain B, Solution Structure Of The Syndecan-4 Whole Cytoplasmic
          Domain
 pdb|1EJQ|A Chain A, Solution Structure Of The Syndecan-4 Whole Cytoplasmic
          Domain In The Presence Of Phosphatidylinositol 4,5-
          Bisphosphate
 pdb|1EJQ|B Chain B, Solution Structure Of The Syndecan-4 Whole Cytoplasmic
          Domain In The Presence Of Phosphatidylinositol 4,5-
          Bisphosphate
          Length = 28

 Score = 26.6 bits (57), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 19/34 (55%), Gaps = 6/34 (17%)

Query: 31 RMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
          RM+KKDEGSY L    + P    Y K    EFYA
Sbjct: 1  RMKKKDEGSYDLG---KKPI---YKKAPTNEFYA 28


>pdb|3LUT|B Chain B, A Structural Model For The Full-Length Shaker Potassium
           Channel Kv1.2
          Length = 499

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 12/20 (60%), Positives = 14/20 (70%)

Query: 9   TVIGGAVVGLLCAILVVMFI 28
           T IGG +VG LCAI  V+ I
Sbjct: 383 TTIGGKIVGSLCAIAGVLTI 402


>pdb|2A79|B Chain B, Mammalian Shaker Kv1.2 Potassium Channel- Beta Subunit
           Complex
          Length = 499

 Score = 25.8 bits (55), Expect = 6.2,   Method: Composition-based stats.
 Identities = 12/20 (60%), Positives = 14/20 (70%)

Query: 9   TVIGGAVVGLLCAILVVMFI 28
           T IGG +VG LCAI  V+ I
Sbjct: 383 TTIGGKIVGSLCAIAGVLTI 402


>pdb|3LNM|B Chain B, F233w Mutant Of The Kv2.1 Paddle-Kv1.2 Chimera Channel
 pdb|3LNM|D Chain D, F233w Mutant Of The Kv2.1 Paddle-Kv1.2 Chimera Channel
          Length = 514

 Score = 25.8 bits (55), Expect = 7.0,   Method: Composition-based stats.
 Identities = 12/20 (60%), Positives = 14/20 (70%)

Query: 9   TVIGGAVVGLLCAILVVMFI 28
           T IGG +VG LCAI  V+ I
Sbjct: 398 TTIGGKIVGSLCAIAGVLTI 417


>pdb|2R9R|B Chain B, Shaker Family Voltage Dependent Potassium Channel
           (Kv1.2-Kv2.1 Paddle Chimera Channel) In Association With
           Beta Subunit
 pdb|2R9R|H Chain H, Shaker Family Voltage Dependent Potassium Channel
           (Kv1.2-Kv2.1 Paddle Chimera Channel) In Association With
           Beta Subunit
          Length = 514

 Score = 25.8 bits (55), Expect = 7.1,   Method: Composition-based stats.
 Identities = 12/20 (60%), Positives = 14/20 (70%)

Query: 9   TVIGGAVVGLLCAILVVMFI 28
           T IGG +VG LCAI  V+ I
Sbjct: 398 TTIGGKIVGSLCAIAGVLTI 417


  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
   0.320    0.133    0.374 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,688,165
Number of Sequences: 62578
Number of extensions: 49320
Number of successful extensions: 85
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 81
Number of HSP's gapped (non-prelim): 5
length of query: 64
length of database: 14,973,337
effective HSP length: 35
effective length of query: 29
effective length of database: 12,783,107
effective search space: 370710103
effective search space used: 370710103
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)