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= 015168
         (412 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 = 29.3 bits (64), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 27/117 (23%), Positives = 50/117 (42%), Gaps = 5/117 (4%)

Query: 259 GVAATFLSAYLVRRLGILKAGAAGLIFQASLLAMAVAVYWSGSLSQQNPLLFFLCLIVLS 318
           G+  T L  ++  ++     GA G+ F  +L+ +A  VYW       NP +  +C+IV+ 
Sbjct: 301 GIPGTLLCGWMSDKVFRGNRGATGVFFM-TLVTIATIVYWMNPAG--NPTVDMICMIVIG 357

Query: 319 RLGHMSYDIVGAQILQTGIPSSKANLIGTTEISVASLVESVMLGVAIIANDVSHFGF 375
            L +    ++G   L+     +     G T   +   +   +   AI+   V  FG+
Sbjct: 358 FLIYGPVMLIGLHALELAPKKAAGTAAGFT--GLFGYLGGSVAASAIVGYTVDFFGW 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
   0.326    0.138    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,694,656
Number of Sequences: 62578
Number of extensions: 391410
Number of successful extensions: 1327
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: 1327
Number of HSP's gapped (non-prelim): 4
length of query: 412
length of database: 14,973,337
effective HSP length: 101
effective length of query: 311
effective length of database: 8,652,959
effective search space: 2691070249
effective search space used: 2691070249
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: 53 (25.0 bits)