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= psy2115
         (77 letters)

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

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



>pdb|1VJR|A Chain A, Crystal Structure Of 4-nitrophenylphosphatase (tm1742)
           From Thermotoga Maritima At 2.40 A Resolution
          Length = 271

 Score = 27.3 bits (59), Expect = 2.3,   Method: Composition-based stats.
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 18  TNPEDIRNNETKPNFV 33
           T PED+   ETKP+FV
Sbjct: 244 TTPEDLERAETKPDFV 259


>pdb|1PW5|A Chain A, Putative Nagd Protein
          Length = 253

 Score = 26.9 bits (58), Expect = 2.7,   Method: Composition-based stats.
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 18  TNPEDIRNNETKPNFV 33
           T PED+   ETKP+FV
Sbjct: 232 TTPEDLERAETKPDFV 247


  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
   0.314    0.135    0.448 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,083,906
Number of Sequences: 62578
Number of extensions: 117580
Number of successful extensions: 284
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 282
Number of HSP's gapped (non-prelim): 4
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)