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= psy5945
         (568 letters)

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

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



>pdb|3DAL|A Chain A, Methyltransferase Domain Of Human Pr Domain-Containing
           Protein 1
 pdb|3DAL|B Chain B, Methyltransferase Domain Of Human Pr Domain-Containing
           Protein 1
          Length = 196

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 24/97 (24%), Positives = 47/97 (48%), Gaps = 13/97 (13%)

Query: 95  FLILVGQINTTDPSSIPADVAHKLTMNYKLSNFSKDEIHHFLESYTKFLFVRHPFERLVS 154
           F  L+G+I T D  ++P +   K    Y    +S+ E+HHF++ + +    +  + R V+
Sbjct: 86  FGPLIGEIYTND--TVPKNANRK----YFWRIYSRGELHHFIDGFNE---EKSNWMRYVN 136

Query: 155 AFHNKLEQSYSSSKYFQSRFGKHIIKTIRTRPTNHSL 191
             H+  EQ+ ++ +   + +      TI+  P N  L
Sbjct: 137 PAHSPREQNLAACQNGMNIY----FYTIKPIPANQEL 169


>pdb|1XF1|A Chain A, Structure Of C5a Peptidase- A Key Virulence Factor From
           Streptococcus
 pdb|1XF1|B Chain B, Structure Of C5a Peptidase- A Key Virulence Factor From
           Streptococcus
          Length = 926

 Score = 30.4 bits (67), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 23/77 (29%)

Query: 72  VDKKHKLLYCYVPKVAC-TNWKRIFLILVGQINTTDPSSIPADVAHKLTMNYKLSNFSKD 130
           VD KH   +   PKV   T+W++I              +IPA+ + ++T+    S FSKD
Sbjct: 528 VDGKH---FALAPKVLYETSWQKI--------------TIPANSSKQVTVPIDASRFSKD 570

Query: 131 EI-----HHFLESYTKF 142
            +      +FLE + +F
Sbjct: 571 LLAQXKNGYFLEGFVRF 587


>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 = 30.0 bits (66), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 31/134 (23%), Positives = 54/134 (40%), Gaps = 23/134 (17%)

Query: 15  DIMKVNAKTYNIPSMNKNWSLTHFERLEYLTSQCLTYKEDLNKSSVLEDEQVLEHILVDK 74
           D  K +A T  +   +   S  H   +       +T     +K   L  +  ++   VD 
Sbjct: 480 DAKKASAATMYVTDKDNTSSKVHLNNVSDKFEVTVTVHNKSDKPQELYYQATVQTDKVDG 539

Query: 75  KHKLLYCYVPKVAC-TNWKRIFLILVGQINTTDPSSIPADVAHKLTMNYKLSNFSKDEI- 132
           KH   +   PK    T+W++I              +IPA+ + ++T+    S FSKD + 
Sbjct: 540 KH---FALAPKALYETSWQKI--------------TIPANSSKQVTVPIDASRFSKDLLA 582

Query: 133 ----HHFLESYTKF 142
                +FLE + +F
Sbjct: 583 QMKNGYFLEGFVRF 596


>pdb|1YF3|A Chain A, T4dam In Complex With Adohcy And 13-Mer Oligonucleotide
           Making Non- And Semi-Specific (~14) CONTACT
 pdb|1YF3|B Chain B, T4dam In Complex With Adohcy And 13-Mer Oligonucleotide
           Making Non- And Semi-Specific (~14) CONTACT
          Length = 259

 Score = 30.0 bits (66), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 109 SIPADVAHKLTMNYKLSNFSKDEIHHFLESYTKFLFVRHPFERLVSAFH---NKLEQSYS 165
           ++  D   K+   YKLS  SK+E     E Y K    R P    V  FH   N +  +Y 
Sbjct: 64  NVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNK---TRDPLLLYVLHFHGFSNMIRINYK 120

Query: 166 SSKYFQSRFGKHIIKTIRTRPTNHSLNHGDDVTF 199
            +  F + FGK  I     +  NH   + D + F
Sbjct: 121 GN--FTTPFGKRTINKNSEKRFNHFKQNCDKIIF 152


>pdb|2Z5E|A Chain A, Crystal Structure Of Proteasome Assembling Chaperone 3
 pdb|2Z5E|B Chain B, Crystal Structure Of Proteasome Assembling Chaperone 3
          Length = 122

 Score = 30.0 bits (66), Expect = 3.9,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 70  ILVDKKHKLLYCYVP-KVACTNWKRIFLILV------GQINTTDPSSIPADVAHKLTMNY 122
           +++ K+   + C VP +V CT +    L++V      G + + +PSS+ +DV+  +    
Sbjct: 6   LVISKQKTEVVCGVPTQVVCTAFSSHILVVVTQFGKMGTLVSLEPSSVASDVSKPVLTTK 65

Query: 123 KLSNFSKDEIHHFLESYTKFL 143
            L    +  IH F ++   F+
Sbjct: 66  VLLGQDEPLIHVFAKNLVAFV 86


  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
   0.318    0.134    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,072,394
Number of Sequences: 62578
Number of extensions: 667705
Number of successful extensions: 1526
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 30
Number of HSP's that attempted gapping in prelim test: 1526
Number of HSP's gapped (non-prelim): 30
length of query: 568
length of database: 14,973,337
effective HSP length: 104
effective length of query: 464
effective length of database: 8,465,225
effective search space: 3927864400
effective search space used: 3927864400
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)