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= psy8365
         (381 letters)

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

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



>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation.
 pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation
          Length = 491

 Score = 38.1 bits (87), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 39/71 (54%)

Query: 61  TTDMHLTNAQYMNLYSWYSWPNVICCFIGGFLIDRVFGIRMGSTIYSVLVVIGQLVFALG 120
           T D+H+T A   ++ + Y+    +   IGGF+ DR+ G R       VL+++G +V AL 
Sbjct: 46  TGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALP 105

Query: 121 AYVDSLFITIL 131
               +LF +I+
Sbjct: 106 FGASALFGSII 116


  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
   0.328    0.141    0.442 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,072,978
Number of Sequences: 62578
Number of extensions: 367706
Number of successful extensions: 792
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 791
Number of HSP's gapped (non-prelim): 1
length of query: 381
length of database: 14,973,337
effective HSP length: 101
effective length of query: 280
effective length of database: 8,652,959
effective search space: 2422828520
effective search space used: 2422828520
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)