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= psy6128
         (529 letters)

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

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



>pdb|3EIF|A Chain A, 1.9 Angstrom Crystal Structure Of The Active Form Of The
           C5a Peptidase From Streptococcus Pyogenes (Scpa)
          Length = 936

 Score = 33.1 bits (74), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 4/82 (4%)

Query: 122 DSGKKSYVFAGEGGPCSLVDSAGPWCCRGGGTEPPTSEHLKDGLCQGMRTQDEMLXXXXX 181
           D  KK++ +A   G  S+V SAG     GG T  P ++H   G+       D  L     
Sbjct: 177 DETKKAFDYAKSKG-VSIVTSAGNDSSFGGKTRLPLADHPDYGVVGTPAAADSTLTVASY 235

Query: 182 X---XXXXXATVKAEDPNSKEM 200
                    ATVK +D  +KEM
Sbjct: 236 SPDKQLTETATVKTDDHQAKEM 257


>pdb|2IPB|A Chain A, Crystal Structure Of T159d Mutant Of S. Typhimurium Phon
           Protein
 pdb|2IPB|B Chain B, Crystal Structure Of T159d Mutant Of S. Typhimurium Phon
           Protein
 pdb|2IPB|C Chain C, Crystal Structure Of T159d Mutant Of S. Typhimurium Phon
           Protein
 pdb|2IPB|D Chain D, Crystal Structure Of T159d Mutant Of S. Typhimurium Phon
           Protein
          Length = 230

 Score = 28.5 bits (62), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 367 CGASFSFGCSWSMYYNGCKYARSKTVRKFRLSVRSEEQEIEEKMHLLATTISP 419
           CGA +        Y    ++AR +T+  F+ S+    +E+ +K +LL+    P
Sbjct: 174 CGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREELNDKNNLLSKEERP 226


  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
   0.317    0.134    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,966,761
Number of Sequences: 62578
Number of extensions: 722443
Number of successful extensions: 1418
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1415
Number of HSP's gapped (non-prelim): 10
length of query: 529
length of database: 14,973,337
effective HSP length: 103
effective length of query: 426
effective length of database: 8,527,803
effective search space: 3632844078
effective search space used: 3632844078
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)