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= 007555
         (598 letters)

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

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



>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
           From E.Coli
          Length = 451

 Score = 30.4 bits (67), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 31/123 (25%), Positives = 52/123 (42%), Gaps = 17/123 (13%)

Query: 445 GVAATFLSAYLVRRLGILKAGAAGLIFQASLLAMAVAVYWSGSLSQQNPLLFFLCLIVLS 504
           G+  T L  ++  ++     GA G+ F  +L+ +A  VYW       NP +  +C+IV+ 
Sbjct: 301 GIPGTLLCGWMSDKVFRGNRGATGVFFM-TLVTIATIVYWMNPAG--NPTVDMICMIVIG 357

Query: 505 RLGHMSYDIVGAQILQ------TGIPSSKANLIGTTEISVASLVESVMLGVAIIANDVSH 558
            L +    ++G   L+       G  +    L G    SVA+         AI+   V  
Sbjct: 358 FLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVAA--------SAIVGYTVDF 409

Query: 559 FGF 561
           FG+
Sbjct: 410 FGW 412


  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
   0.323    0.135    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,346,289
Number of Sequences: 62578
Number of extensions: 575945
Number of successful extensions: 1402
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: 1402
Number of HSP's gapped (non-prelim): 4
length of query: 598
length of database: 14,973,337
effective HSP length: 104
effective length of query: 494
effective length of database: 8,465,225
effective search space: 4181821150
effective search space used: 4181821150
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)