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= psy15808
         (275 letters)

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

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



>pdb|2NR9|A Chain A, Crystal Structure Of Glpg, Rhomboid Peptidase From
           Haemophilus Influenzae
 pdb|3ODJ|A Chain A, Crystal Structure Of H. Influenzae Rhomboid Glpg With
           Disordered Loop 4, Helix 5 And Loop 5
          Length = 196

 Score = 29.3 bits (64), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 71  RLVLSALEHGDDMHLYYNMVSLIVKGRELERMFGSVQFVVLVSFLIISTSVCYV 124
           R +   L H  ++H+ +N+    + G  +ER FGSV+ ++L  +++ S    YV
Sbjct: 52  RYISHTLVHLSNLHILFNLSWFFIFGGMIERTFGSVKLLML--YVVASAITGYV 103


>pdb|3MKB|A Chain A, Crystal Structure Determination Of Shortfin Mako (Isurus
          Oxyrinchus) Hemoglobin At 1.9 Angstrom Resolution
 pdb|3MKB|C Chain C, Crystal Structure Determination Of Shortfin Mako (Isurus
          Oxyrinchus) Hemoglobin At 1.9 Angstrom Resolution
          Length = 140

 Score = 27.7 bits (60), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 71 RLVLSALEHGDDMHLYYNMVSLIVKGREL 99
          R V+SA EH DD+H +  MV  +  G++L
Sbjct: 64 RAVVSAAEHDDDLHAHL-MVLAVTHGKKL 91


  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    0.139    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,927,597
Number of Sequences: 62578
Number of extensions: 186828
Number of successful extensions: 344
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: 343
Number of HSP's gapped (non-prelim): 2
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)