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= 041738
         (96 letters)

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

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



>pdb|1K66|A Chain A, Crystal Structure Of The Cyanobacterial Phytochrome
          Response Regulator, Rcpb
 pdb|1K66|B Chain B, Crystal Structure Of The Cyanobacterial Phytochrome
          Response Regulator, Rcpb
          Length = 149

 Score = 30.0 bits (66), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 11/20 (55%), Positives = 14/20 (70%)

Query: 31 QRHFQRQGISGPGYRLITGN 50
          QR  QR+G+  P YR ITG+
Sbjct: 23 QRLLQREGVVNPIYRCITGD 42


>pdb|2W9S|A Chain A, Staphylococcus Aureus S1:dhfr In Complex With
          Trimethoprim
 pdb|2W9S|B Chain B, Staphylococcus Aureus S1:dhfr In Complex With
          Trimethoprim
 pdb|2W9S|C Chain C, Staphylococcus Aureus S1:dhfr In Complex With
          Trimethoprim
 pdb|2W9S|D Chain D, Staphylococcus Aureus S1:dhfr In Complex With
          Trimethoprim
 pdb|2W9S|E Chain E, Staphylococcus Aureus S1:dhfr In Complex With
          Trimethoprim
 pdb|2W9S|F Chain F, Staphylococcus Aureus S1:dhfr In Complex With
          Trimethoprim
 pdb|2W9T|A Chain A, Staphylococcus Aureus S1:dhfr
 pdb|2W9T|B Chain B, Staphylococcus Aureus S1:dhfr
          Length = 161

 Score = 26.9 bits (58), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 13/43 (30%), Positives = 23/43 (53%)

Query: 45 RLITGNSTEISRMHIEALSKPISPVDHDILHRTAPFYHRWSRV 87
          +L TGN+  ++R   E++ KP+    + +L   A F+H    V
Sbjct: 34 QLTTGNTLVMARKTFESIGKPLPNRRNVVLTNQASFHHEGVDV 76


>pdb|1RC6|A Chain A, Crystal Structure Of Protein Ylba From E. Coli, Pfam
           Duf861
 pdb|1RC6|B Chain B, Crystal Structure Of Protein Ylba From E. Coli, Pfam
           Duf861
          Length = 261

 Score = 25.4 bits (54), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 11/35 (31%), Positives = 22/35 (62%), Gaps = 2/35 (5%)

Query: 34  FQRQGISGPGYR--LITGNSTEISRMHIEALSKPI 66
           ++R+ +   GY   L++GN++E+ R+H E +   I
Sbjct: 132 YKRRYVPVEGYAPWLVSGNASELERIHYEGMDDVI 166


  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    0.140    0.475 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,706,121
Number of Sequences: 62578
Number of extensions: 88772
Number of successful extensions: 242
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 240
Number of HSP's gapped (non-prelim): 6
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
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: 45 (21.9 bits)