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= 028389
         (209 letters)

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

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



>pdb|2WBR|A Chain A, The Rrm Domain In Gw182 Proteins Contributes To Mirna-
           Mediated Gene Silencing
          Length = 89

 Score = 28.5 bits (62), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 9/23 (39%), Positives = 18/23 (78%)

Query: 125 CVVGSTTIVLHAPAEREIESVIE 147
           CV+ +TTI   +P+E E++S+++
Sbjct: 66  CVLANTTIFAESPSENEVQSIMQ 88


>pdb|3FDH|A Chain A, Crystal Structure Of A SusdRAGB FAMILY PROTEIN (BT_2033)
           FROM Bacteroides Thetaiotaomicron Vpi-5482 At 1.75 A
           Resolution
          Length = 499

 Score = 27.7 bits (60), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 1/20 (5%)

Query: 50  VRAGFGGYSYLY-EPLWWVG 68
           V+A +G   Y+Y EP+WW G
Sbjct: 477 VKAAYGNGDYVYSEPVWWAG 496


>pdb|3S1S|A Chain A, Characterization And Crystal Structure Of The Type Iig
           Restriction Endonuclease Bpusi
          Length = 878

 Score = 27.7 bits (60), Expect = 4.8,   Method: Composition-based stats.
 Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 2/34 (5%)

Query: 166 IFHYIPQYGQTHIMVYIGVCSLVGSLSVCILHTG 199
           +F Y+P YG   + VY  +C    +L+  +++TG
Sbjct: 10  VFSYLPSYGDDEVSVYHPICE--AALNQALVNTG 41


  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
   0.327    0.144    0.461 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,704,437
Number of Sequences: 62578
Number of extensions: 128155
Number of successful extensions: 243
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 242
Number of HSP's gapped (non-prelim): 3
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)