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= 007043
         (620 letters)

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

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



>pdb|4B93|A Chain A, Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyrin
           Repeat Domain Of Varp
          Length = 189

 Score = 29.6 bits (65), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 10/79 (12%)

Query: 25  ERDRALDELHEMKRMAQEANMRLSETMSTR-KAADIYTMNETLSKELKVKEKNIESLKKE 83
           ER RA   L+E+K+       R   T  +R + A  Y MN   S  L  + K+  S  K 
Sbjct: 72  ERSRAFSFLNEVKK-------RFQTTYGSRAQTALPYAMNSEFSSVLAAQLKH-HSENKS 123

Query: 84  WEIKLVEKDASLDELKGTL 102
            + K++E  A +DELKG +
Sbjct: 124 LD-KVMETQAQVDELKGIM 141


>pdb|3V4Y|B Chain B, Crystal Structure Of The First Nuclear Pp1 Holoenzyme
 pdb|3V4Y|D Chain D, Crystal Structure Of The First Nuclear Pp1 Holoenzyme
 pdb|3V4Y|F Chain F, Crystal Structure Of The First Nuclear Pp1 Holoenzyme
 pdb|3V4Y|H Chain H, Crystal Structure Of The First Nuclear Pp1 Holoenzyme
          Length = 62

 Score = 28.9 bits (63), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 12/21 (57%), Positives = 17/21 (80%)

Query: 556 RKNSSVSFSDDGKTIIPDDLD 576
           RKNS V+FS+D + I P+D+D
Sbjct: 42  RKNSRVTFSEDDEIINPEDVD 62


  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
   0.308    0.124    0.321 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,144,249
Number of Sequences: 62578
Number of extensions: 452078
Number of successful extensions: 1561
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1522
Number of HSP's gapped (non-prelim): 50
length of query: 620
length of database: 14,973,337
effective HSP length: 105
effective length of query: 515
effective length of database: 8,402,647
effective search space: 4327363205
effective search space used: 4327363205
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (25.4 bits)