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= psy9948
         (203 letters)

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

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



>pdb|2V5D|A Chain A, Structure Of A Family 84 Glycoside Hydrolase And A Family
           32 Carbohydrate-Binding Module In Tandem From
           Clostridium Perfringens
          Length = 737

 Score = 29.3 bits (64), Expect = 1.6,   Method: Composition-based stats.
 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 7/90 (7%)

Query: 116 AQIGISVEPIEVVNQHLASKSNESLSNFVQFCQKMVTSFVNYISSFSTTQASMVPNPNET 175
           AQ+    E  E   +   +K N +LS+F    +K+  SF+    SF  T    + NP   
Sbjct: 544 AQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLT----LINPRTV 599

Query: 176 YVPISSVQNWYQNFERKLALNPN---FWQS 202
            +  SS +   +N     A + +   FW S
Sbjct: 600 KITASSEETSGENAPASFASDGDMNTFWHS 629


>pdb|3PSI|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(239-1451)
          Length = 1219

 Score = 26.6 bits (57), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 13/43 (30%), Positives = 19/43 (44%)

Query: 136 SNESLSNFVQFCQKMVTSFVNYISSFSTTQASMVPNPNETYVP 178
           S E   N  + CQK+V   V +       QA  +PN  +  +P
Sbjct: 474 SQEVKDNLTKNCQKLVAKTVRHKFMTKLDQAPFIPNVRDPKIP 516


  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
   0.316    0.130    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,266,226
Number of Sequences: 62578
Number of extensions: 174179
Number of successful extensions: 423
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 417
Number of HSP's gapped (non-prelim): 8
length of query: 203
length of database: 14,973,337
effective HSP length: 94
effective length of query: 109
effective length of database: 9,091,005
effective search space: 990919545
effective search space used: 990919545
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)