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= psy7377
         (83 letters)

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

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



>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
          Putative Rna-Binding Protein 11
          Length = 95

 Score = 26.6 bits (57), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 8/25 (32%), Positives = 20/25 (80%)

Query: 11 FPSEEEADKVLSIPDVEQRIKDVLM 35
          FP++EEAD+ + + ++E R+++ ++
Sbjct: 9  FPAQEEADRTVFVGNLEARVREEIL 33


>pdb|3EFY|A Chain A, Structure Of The Cyclomodulin Cif From Pathogenic
           Escherichia Coli
 pdb|3EFY|B Chain B, Structure Of The Cyclomodulin Cif From Pathogenic
           Escherichia Coli
          Length = 195

 Score = 25.8 bits (55), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 3/32 (9%)

Query: 54  TSLLLKDLCTYF---SYNEFLMERIMQIFPLD 82
           T +LL D+C YF   S N+  +E+I  +F +D
Sbjct: 109 TPILLDDICNYFSCMSQNKTDLEQIATLFDID 140


>pdb|3TL2|A Chain A, Crystal Structure Of Bacillus Anthracis Str. Ames Malate
           Dehydrogenase In Closed Conformation
          Length = 315

 Score = 25.8 bits (55), Expect = 6.5,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 32  DVLMVLGNFKQYRDPARSRCEYTSLLLKD 60
           +++ +LGN   Y  PA S  E T  +LKD
Sbjct: 223 EIVGLLGNGSAYYAPAASLVEMTEAILKD 251


  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
   0.324    0.140    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,326,915
Number of Sequences: 62578
Number of extensions: 73718
Number of successful extensions: 242
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 239
Number of HSP's gapped (non-prelim): 5
length of query: 83
length of database: 14,973,337
effective HSP length: 51
effective length of query: 32
effective length of database: 11,781,859
effective search space: 377019488
effective search space used: 377019488
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)