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= 041687
         (764 letters)

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

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



>pdb|2ZUQ|A Chain A, Crystal Structure Of Dsbb-Fab Complex
 pdb|2ZUQ|D Chain D, Crystal Structure Of Dsbb-Fab Complex
 pdb|2LTQ|A Chain A, High Resolution Structure Of Dsbb C41s By Joint
           Calculation With Solid-state Nmr And X-ray Data
 pdb|2LTQ|D Chain D, High Resolution Structure Of Dsbb C41s By Joint
           Calculation With Solid-state Nmr And X-ray Data
          Length = 176

 Score = 32.3 bits (72), Expect = 0.94,   Method: Composition-based stats.
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 2/39 (5%)

Query: 277 LWFVNIMLLGCSLLA--EITGLHGYFGAVILGINTPATP 313
           LWF ++MLL  S+L   E   L G  GA ++G   P TP
Sbjct: 30  LWFQHVMLLKPSVLCIYERVALFGVLGAALIGAIAPKTP 68


>pdb|3R4V|A Chain A, Structure Of The Phage Tubulin Phuz-gdp
          Length = 315

 Score = 28.9 bits (63), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 18/25 (72%)

Query: 150 SFVKGAIQLEENLGNSLKTVAALES 174
           SFV GA++  +NLGN + T+  LE+
Sbjct: 115 SFVVGAMESTDNLGNDIDTMKTLEA 139


  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
   0.325    0.138    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,029,794
Number of Sequences: 62578
Number of extensions: 700456
Number of successful extensions: 1681
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1681
Number of HSP's gapped (non-prelim): 5
length of query: 764
length of database: 14,973,337
effective HSP length: 106
effective length of query: 658
effective length of database: 8,340,069
effective search space: 5487765402
effective search space used: 5487765402
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.8 bits)