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= 004549
         (745 letters)

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

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



>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
 pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
          Length = 1054

 Score = 32.0 bits (71), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 491 LDVPARKRFAKYRGLKSFRTSSWDPKESLPPEYARIFAF 529
           LD+P R RFA + G  SFR +  D  +SL P+  ++ A+
Sbjct: 337 LDLPERIRFAVFVGCPSFRVTIEDI-DSLSPQMVKLLAY 374


>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
          Length = 1054

 Score = 31.6 bits (70), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 491 LDVPARKRFAKYRGLKSFRTSSWDPKESLPPEYARIFAF 529
           LD+P R RFA + G  SFR +  D  +SL P+  ++ A+
Sbjct: 337 LDLPERIRFAVFVGCPSFRVTIEDI-DSLSPQMVKLLAY 374


  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
   0.319    0.134    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,396,637
Number of Sequences: 62578
Number of extensions: 735220
Number of successful extensions: 1656
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1656
Number of HSP's gapped (non-prelim): 3
length of query: 745
length of database: 14,973,337
effective HSP length: 106
effective length of query: 639
effective length of database: 8,340,069
effective search space: 5329304091
effective search space used: 5329304091
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)