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= 018552
         (354 letters)

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

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



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 50/99 (50%), Gaps = 3/99 (3%)

Query: 32  LYTVLYITGFGAAGIRPCVSSFGADQFDERSKDYKTHLDRFFNFFYLSVTVGAIVAFTLV 91
            YT L++   G+ GI+P VSSF  DQFD+ +K       + F+ FY ++  G+  A   +
Sbjct: 112 FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLA---QKAFDMFYFTINFGSFFASLSM 168

Query: 92  VYIQMEHGWGSAFGALAIAMGISNMLFFIGTPLYRHRLP 130
             +    G   AFG   + M ++ + F++G   Y H  P
Sbjct: 169 PLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPP 207


  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    0.136    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,535,659
Number of Sequences: 62578
Number of extensions: 355050
Number of successful extensions: 519
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 514
Number of HSP's gapped (non-prelim): 7
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
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: 52 (24.6 bits)