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= psy4521
         (223 letters)

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

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



>pdb|3TW8|A Chain A, Gef Domain Of Dennd 1b In Complex With Rab Gtpase Rab35
 pdb|3TW8|C Chain C, Gef Domain Of Dennd 1b In Complex With Rab Gtpase Rab35
          Length = 391

 Score = 27.3 bits (59), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 33/134 (24%), Positives = 55/134 (41%), Gaps = 15/134 (11%)

Query: 91  LPCLEEY----NKLYLWFGKDHESTRVFSSKLNEKRCFLIRETENQPLPTESKAKGLDLN 146
           LP  E Y    N L  +  K+ E+       LNE     +R   N P+P  +    L ++
Sbjct: 102 LPWFEVYYKLLNTLADYLAKELEN------DLNET----LRSLYNHPVPKANTPVNLSVH 151

Query: 147 RIIESASPLCHPAIITYDVLQEDVLA-DLQNVTLLLLRTMYCRRMCWLTYKTTNRFKVSN 205
               +      P I     L E  +A D+ N+  L    ++ RR+  ++ K +      +
Sbjct: 152 SYFIAPDVTGLPTIPESRNLTEYFVAVDVNNMLQLYASMLHERRIVIISSKLSTLTACIH 211

Query: 206 GNAFRLCPEFWEVI 219
           G+A  L P +W+ I
Sbjct: 212 GSAALLYPMYWQHI 225


  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
   0.321    0.136    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,429,788
Number of Sequences: 62578
Number of extensions: 244751
Number of successful extensions: 460
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 460
Number of HSP's gapped (non-prelim): 2
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)