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= 007012
         (621 letters)

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

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



>pdb|3CGY|A Chain A, Crystal Structure Of Salmonella Sensor Kinase Phoq
           Catalytic Domain In Complex With Radicicol
 pdb|3CGY|B Chain B, Crystal Structure Of Salmonella Sensor Kinase Phoq
           Catalytic Domain In Complex With Radicicol
 pdb|3CGY|C Chain C, Crystal Structure Of Salmonella Sensor Kinase Phoq
           Catalytic Domain In Complex With Radicicol
 pdb|3CGZ|A Chain A, Crystal Structure Of Salmonella Sensor Kinase Phoq
           Catalytic Domain
 pdb|3CGZ|B Chain B, Crystal Structure Of Salmonella Sensor Kinase Phoq
           Catalytic Domain
 pdb|3CGZ|C Chain C, Crystal Structure Of Salmonella Sensor Kinase Phoq
           Catalytic Domain
          Length = 157

 Score = 30.8 bits (68), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 13/84 (15%)

Query: 527 VVIDDDGPDMHYMMHSLTPFGSELFSENMVEDNMTWNFVAGLTVARELLESYGCVVRVIS 586
           + ++DDGP + +   SL      +F      D +      GL VARE+ E Y   +    
Sbjct: 82  IFVEDDGPGIPHSKRSL------VFDRGQRADTLRPGQGVGLAVAREITEQYAGQI---- 131

Query: 587 PWKTDAALGSGGTRVELWLPSPAP 610
              +D+ L  GG R+E+      P
Sbjct: 132 -IASDSLL--GGARMEVVFGRQHP 152


>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 1752

 Score = 30.0 bits (66), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 493  RQALSNLIEGALMRTQVGGKVEIVSAAAPAGDALVVIDD-DGPDMHYMMHSLTPFGSELF 551
            R  ++    GALMR      VEI+  AA +G+     DD  G   + M+  L P G+  F
Sbjct: 1392 RHGINRAETGALMRCSFEETVEILMDAAASGEK----DDCKGISENIMLGQLAPMGTGAF 1447

Query: 552  SENMVEDNMTWNFVAGLTV 570
               + +D M  N+  G  V
Sbjct: 1448 DIYLDQD-MLMNYSLGTAV 1465


  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
   0.318    0.132    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,799,156
Number of Sequences: 62578
Number of extensions: 572892
Number of successful extensions: 1164
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1163
Number of HSP's gapped (non-prelim): 7
length of query: 621
length of database: 14,973,337
effective HSP length: 105
effective length of query: 516
effective length of database: 8,402,647
effective search space: 4335765852
effective search space used: 4335765852
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: 54 (25.4 bits)