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= 041509
         (211 letters)

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

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



>pdb|1VE3|A Chain A, Crystal Structure Of Ph0226 Protein From Pyrococcus
           Horikoshii Ot3
 pdb|1VE3|B Chain B, Crystal Structure Of Ph0226 Protein From Pyrococcus
           Horikoshii Ot3
          Length = 227

 Score = 30.8 bits (68), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 34/145 (23%), Positives = 60/145 (41%), Gaps = 41/145 (28%)

Query: 74  LRRVEEYKLSKKILGLDASHVEFVIGDAQSLLLSHFREADFVLIDCNLENHEG-----VL 128
           +R+  EY  S++      S+VEF++GDA+ L     +  D+V+   ++ + E      V 
Sbjct: 73  IRKAREYAKSRE------SNVEFIVGDARKLSFED-KTFDYVIFIDSIVHFEPLELNQVF 125

Query: 129 RAVQAGNKPNGAVVVGYNAFXXXXXXXXXXXXQLLPIGEGLLVTRIAAASANKKSHWIVK 188
           + V+   KP+G  +  +               +LLP        R+  +    + +WI K
Sbjct: 126 KEVRRVLKPSGKFIXYFTDL-----------RELLP--------RLKESLVVGQKYWISK 166

Query: 189 ----------VDKCTGEEHVFRVRF 203
                     V +   E+  FRVRF
Sbjct: 167 VIPDQEERTVVIEFKSEQDSFRVRF 191


  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
   0.320    0.134    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,991,073
Number of Sequences: 62578
Number of extensions: 157794
Number of successful extensions: 263
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 263
Number of HSP's gapped (non-prelim): 1
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)