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= 032137
         (146 letters)

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

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



>pdb|3KAE|A Chain A, Cdc27 N-Terminus
 pdb|3KAE|B Chain B, Cdc27 N-Terminus
 pdb|3KAE|C Chain C, Cdc27 N-Terminus
 pdb|3KAE|D Chain D, Cdc27 N-Terminus
          Length = 242

 Score = 28.1 bits (61), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)

Query: 69  KLDKGPDF-ATPEEIFDDPSDVELYRSLIG 97
           K+++ PD  A  +E+F DP D E + SL+G
Sbjct: 92  KVERDPDVDARIQEMFVDPGDEEFFESLLG 121


>pdb|3ME5|A Chain A, Crystal Structure Of Putative Dna Cytosine Methylase From
           Shigella Flexneri 2a Str. 2457t
          Length = 482

 Score = 26.2 bits (56), Expect = 6.5,   Method: Composition-based stats.
 Identities = 12/22 (54%), Positives = 15/22 (68%)

Query: 65  GACCKLDKGPDFATPEEIFDDP 86
           GA   +D+G D AT E+ FDDP
Sbjct: 373 GAEILIDRGWDXATGEKDFDDP 394


>pdb|3LX6|A Chain A, Crystal Structure Of Putative Dna Cytosine Methylase From
           Shigella Flexneri 2a Str. 2457t
 pdb|3LX6|B Chain B, Crystal Structure Of Putative Dna Cytosine Methylase From
           Shigella Flexneri 2a Str. 2457t
          Length = 410

 Score = 25.8 bits (55), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 12/22 (54%), Positives = 15/22 (68%)

Query: 65  GACCKLDKGPDFATPEEIFDDP 86
           GA   +D+G D AT E+ FDDP
Sbjct: 311 GAEILIDRGWDXATGEKDFDDP 332


  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
   0.323    0.140    0.460 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,993,660
Number of Sequences: 62578
Number of extensions: 155677
Number of successful extensions: 220
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 218
Number of HSP's gapped (non-prelim): 3
length of query: 146
length of database: 14,973,337
effective HSP length: 90
effective length of query: 56
effective length of database: 9,341,317
effective search space: 523113752
effective search space used: 523113752
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)