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= 036090
         (177 letters)

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

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



>pdb|3NUH|B Chain B, A Domain Insertion In E. Coli Gyrb Adopts A Novel Fold
           That Plays A Critical Role In Gyrase Function
          Length = 420

 Score = 27.7 bits (60), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 10/63 (15%)

Query: 125 PCPGFLASGGRYRR--------QGQTMDEVAFGRGEKRAPVSSDSENID--PSKSRGGRK 174
           P      +GG YRR        +G   ++    RGE+R PV+S  + +D    +SR G  
Sbjct: 292 PLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLS 351

Query: 175 FKR 177
            +R
Sbjct: 352 IQR 354


  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
   0.315    0.132    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,406,594
Number of Sequences: 62578
Number of extensions: 227375
Number of successful extensions: 479
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 479
Number of HSP's gapped (non-prelim): 1
length of query: 177
length of database: 14,973,337
effective HSP length: 92
effective length of query: 85
effective length of database: 9,216,161
effective search space: 783373685
effective search space used: 783373685
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)