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= 019938
         (333 letters)

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

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



>pdb|1VR5|A Chain A, Crystal Structure Of Oligopeptide Abc Transporter,
           Periplasmic Oligopeptide-Binding (Tm1223) From
           Thermotoga Maritima At 1.73 A Resolution
 pdb|1VR5|B Chain B, Crystal Structure Of Oligopeptide Abc Transporter,
           Periplasmic Oligopeptide-Binding (Tm1223) From
           Thermotoga Maritima At 1.73 A Resolution
          Length = 547

 Score = 32.3 bits (72), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 14/96 (14%)

Query: 213 DGTSRCPDEMVRRIRVTSSYEDTS------WNGKLLETYDTQTDRFVIAPCRWTVRKLHI 266
           DG     D++V    +   Y   S      W G++ E  D +T +FV +  R+   K  +
Sbjct: 89  DGVPLTADDVVFTFEIAKKYTGISYSPVWNWLGRI-ERVDERTLKFVFSDPRYQEWKQXL 147

Query: 267 VMS-------LQQLSDEEILRRCSTSPSAEGPDFVE 295
           + +        +  ++EE+L+  + +P   GP +VE
Sbjct: 148 INTPIVPKHIWENKTEEEVLQAANENPVGSGPYYVE 183


  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
   0.321    0.135    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,720,667
Number of Sequences: 62578
Number of extensions: 393555
Number of successful extensions: 804
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: 804
Number of HSP's gapped (non-prelim): 1
length of query: 333
length of database: 14,973,337
effective HSP length: 99
effective length of query: 234
effective length of database: 8,778,115
effective search space: 2054078910
effective search space used: 2054078910
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)