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= psy1953
         (379 letters)

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

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



>pdb|3GHG|A Chain A, Crystal Structure Of Human Fibrinogen
 pdb|3GHG|D Chain D, Crystal Structure Of Human Fibrinogen
 pdb|3GHG|G Chain G, Crystal Structure Of Human Fibrinogen
 pdb|3GHG|J Chain J, Crystal Structure Of Human Fibrinogen
          Length = 562

 Score = 29.3 bits (64), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 16/70 (22%), Positives = 27/70 (38%)

Query: 116 RNHRLINEIFXXXXXXXXXXXXTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKR 175
           R ++L N +F            TTN M++L+    S            + +  + E  KR
Sbjct: 65  RINKLKNSLFEYQKNNKDSHSLTTNIMEILRGDFSSANNRDNTYNRVSEDLRSRIEVLKR 124

Query: 176 KFVESSEQFQ 185
           K +E  +  Q
Sbjct: 125 KVIEKVQHIQ 134


>pdb|2KD3|A Chain A, Nmr Structure Of The Wnt Modulator Protein Sclerostin
          Length = 113

 Score = 28.1 bits (61), Expect = 9.5,   Method: Composition-based stats.
 Identities = 9/11 (81%), Positives = 10/11 (90%)

Query: 314 HMNAGRPPHYP 324
           HMN GRPPH+P
Sbjct: 3   HMNGGRPPHHP 13


  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
   0.316    0.132    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,727,971
Number of Sequences: 62578
Number of extensions: 260706
Number of successful extensions: 703
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 697
Number of HSP's gapped (non-prelim): 6
length of query: 379
length of database: 14,973,337
effective HSP length: 100
effective length of query: 279
effective length of database: 8,715,537
effective search space: 2431634823
effective search space used: 2431634823
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)