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= 013983
         (432 letters)

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

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



>pdb|3NVQ|A Chain A, Molecular Mechanism Of Guidance Cue Recognition
 pdb|3NVQ|E Chain E, Molecular Mechanism Of Guidance Cue Recognition
          Length = 590

 Score = 32.7 bits (73), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 183 DVELYYTFNITNKAVISRIVMNQT--LYVRRRFIWNKATQSWELYSDVPRDQCDTYGLCG 240
           + E  + FNI       R    QT  L   RR ++   +  WE+ S VP D C+ YG  G
Sbjct: 400 EQEHSFAFNIMEIQPFRRAAAIQTMSLDAERRKLY--VSSQWEV-SQVPLDLCEVYG-GG 455

Query: 241 AYGICIIGQSPVC 253
            +G C++ + P C
Sbjct: 456 CHG-CLMSRDPYC 467


>pdb|3APO|A Chain A, Crystal Structure Of Full-Length Erdj5
          Length = 780

 Score = 28.5 bits (62), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 38/139 (27%), Positives = 58/139 (41%), Gaps = 15/139 (10%)

Query: 43  VLTSQSNIVVWSAYLSKE--------VQTPVVLQLLDS--GNLVLRDEHDGDSETYFWQS 92
           V+ +QS+I  +  + S E        ++ P V+ L  S    LV + +HD      F+  
Sbjct: 514 VVFNQSSIHEYEGHHSAEQILEFIEDLRNPSVVSLTPSTFNELVKQRKHDEVWMVDFYSP 573

Query: 93  FDYPSDTLLPGMKLGWDLKTGLERRVTSWKSFDDPSPGDFIWAIERQDNPEVVMW-KGSR 151
           + +PS  L+P  K      TGL     +  S D      F      Q  PE+  + + S 
Sbjct: 574 WSHPSQVLMPEWKRMARTLTGL----INVGSVDCGQYHSFCTQENVQRYPEIRFYPQKSS 629

Query: 152 KFYRTGPWNGLRFSAPSLR 170
           K Y+   +NG    A SLR
Sbjct: 630 KAYQYHSYNGWNRDAYSLR 648


  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
   0.322    0.138    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,798,657
Number of Sequences: 62578
Number of extensions: 603701
Number of successful extensions: 940
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 939
Number of HSP's gapped (non-prelim): 4
length of query: 432
length of database: 14,973,337
effective HSP length: 102
effective length of query: 330
effective length of database: 8,590,381
effective search space: 2834825730
effective search space used: 2834825730
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: 53 (25.0 bits)