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= psy14933
         (100 letters)

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

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



>pdb|1ZRT|C Chain C, Rhodobacter Capsulatus Cytochrome Bc1 Complex With
           Stigmatellin Bound
 pdb|1ZRT|P Chain P, Rhodobacter Capsulatus Cytochrome Bc1 Complex With
           Stigmatellin Bound
          Length = 437

 Score = 27.3 bits (59), Expect = 2.0,   Method: Composition-based stats.
 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 19/69 (27%)

Query: 28  TGDLDQAFKSIAFITRLDVACICLGNMRDIQGIWTLRYAQAEPELEARVAALAIHLQ--- 84
           T  +D AF S+  I            MRD+ G W +RY  A     A +  LA+++    
Sbjct: 70  TPHVDLAFASVEHI------------MRDVNGGWAMRYIHAN---GASLFFLAVYIHIFR 114

Query: 85  -LYVSDYSA 92
            LY   Y A
Sbjct: 115 GLYYGSYKA 123


>pdb|2Y3M|A Chain A, Structure Of The Extra-Membranous Domain Of The Secretin
          Hofq From Actinobacillus Actinomycetemcomitans
 pdb|2Y3M|B Chain B, Structure Of The Extra-Membranous Domain Of The Secretin
          Hofq From Actinobacillus Actinomycetemcomitans
          Length = 175

 Score = 26.2 bits (56), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 23 SYYLNTGDLDQAFKSIAFITRLDV 46
          S  L   DLDQ F+S+A I +LD+
Sbjct: 43 SLQLENVDLDQLFRSVAKIKQLDL 66


  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
   0.327    0.139    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,683,967
Number of Sequences: 62578
Number of extensions: 84956
Number of successful extensions: 206
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 205
Number of HSP's gapped (non-prelim): 2
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
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: 45 (21.9 bits)