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= psy5514
         (124 letters)

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

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



>pdb|3AXH|A Chain A, Crystal Structure Of Isomaltase In Complex With Isomaltose
 pdb|3AXI|A Chain A, Crystal Structure Of Isomaltase In Complex With Maltose
          Length = 589

 Score = 28.5 bits (62), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 6   TVNVYGSCKQLHITQLFKIGHTEVGTLGVCRY 37
           T  +Y S  +  +++LF   HT+VGT  + RY
Sbjct: 285 TKRLYTSASRHELSELFNFSHTDVGTSPLFRY 316


>pdb|3A47|A Chain A, Crystal Structure Of Isomaltase From Saccharomyces
           Cerevisiae
 pdb|3A4A|A Chain A, Crystal Structure Of Isomaltase From Saccharomyces
           Cerevisiae
 pdb|3AJ7|A Chain A, Crystal Structure Of Isomaltase From Saccharomyces
           Cerevisiae
          Length = 589

 Score = 28.5 bits (62), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 6   TVNVYGSCKQLHITQLFKIGHTEVGTLGVCRY 37
           T  +Y S  +  +++LF   HT+VGT  + RY
Sbjct: 285 TKRLYTSASRHELSELFNFSHTDVGTSPLFRY 316


>pdb|3UPU|A Chain A, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
 pdb|3UPU|B Chain B, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
 pdb|3UPU|C Chain C, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
          Length = 459

 Score = 27.7 bits (60), Expect = 1.7,   Method: Composition-based stats.
 Identities = 15/26 (57%), Positives = 15/26 (57%)

Query: 28  EVGTLGVCRYLGCLGVSRYLRKLFGI 53
           EV  L  CR L C  VS Y RKLF I
Sbjct: 122 EVPDLAKCRVLICDEVSXYDRKLFKI 147


>pdb|1C76|A Chain A, Staphylokinase (Sak) Monomer
 pdb|1C77|A Chain A, Staphylokinase (Sak) Dimer
 pdb|1C77|B Chain B, Staphylokinase (Sak) Dimer
 pdb|1C78|A Chain A, Staphylokinase (Sak) Dimer
 pdb|1C78|B Chain B, Staphylokinase (Sak) Dimer
 pdb|1C79|A Chain A, Staphylokinase (Sak) Dimer
 pdb|1C79|B Chain B, Staphylokinase (Sak) Dimer
          Length = 136

 Score = 27.7 bits (60), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 89  PQLILCVYGLDGFGNDVIRGYGLCHLPISSGTT 121
           P L++ V G+DG GN+++  +     PI  GTT
Sbjct: 23  PYLMVNVTGVDGKGNELLSPH-YVEFPIKPGTT 54


  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
   0.326    0.144    0.478 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,000,091
Number of Sequences: 62578
Number of extensions: 159176
Number of successful extensions: 333
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 330
Number of HSP's gapped (non-prelim): 4
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)