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= psy6677
         (320 letters)

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

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



>pdb|3UPG|A Chain A, Loop Deletion Mutant Of Salmonella Typhi Osmoporin
           (Ompc):an Outer Membrane Protein
          Length = 338

 Score = 30.0 bits (66), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 253 DRSTAETPSLHSPTDRSTVETPSLPNHPDLNIYLSIALSKFRRSTRDDRQEFGAVLQNFG 312
           D++      L+   DR+TV T  L    + NIYL+   S+   +TR     F    QNF 
Sbjct: 190 DQNNTANARLYGNGDRATVYTGGLKYDAN-NIYLAAQYSQTYNATRFGTSGFANKAQNFE 248

Query: 313 AVLQ 316
            V Q
Sbjct: 249 VVAQ 252


  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
   0.302    0.121    0.353 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,637,762
Number of Sequences: 62578
Number of extensions: 556409
Number of successful extensions: 955
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 611
Number of HSP's gapped (non-prelim): 86
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
T: 11
A: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 51 (24.3 bits)