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= psy18121
         (109 letters)

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

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



>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
           Gorgonarius In Complex With Hypoxanthine-Containing Dna
          Length = 773

 Score = 25.8 bits (55), Expect = 6.0,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 18  ARSLERILEEAHLSGELNLSGRKLKDFPNSGGKYDLSDSVIVVYFSRSGRKLKDFPNSG 76
           AR LE IL+     G++  + R +K+      KY++    +V+Y  +  R LKD+  +G
Sbjct: 624 ARVLEAILKH----GDVEEAVRIVKEVTEKLSKYEVPPEKLVIY-EQITRDLKDYKATG 677


>pdb|2O7I|A Chain A, The X-Ray Crystal Structure Of A Thermophilic Cellobiose
           Binding Protein Bound With Cellobiose
 pdb|3I5O|A Chain A, The X-Ray Crystal Structure Of A Thermophilic Cellobiose
           Binding Protein Bound With Cellopentaose
 pdb|3I5O|B Chain B, The X-Ray Crystal Structure Of A Thermophilic Cellobiose
           Binding Protein Bound With Cellopentaose
          Length = 592

 Score = 25.8 bits (55), Expect = 6.0,   Method: Composition-based stats.
 Identities = 15/27 (55%), Positives = 17/27 (62%), Gaps = 1/27 (3%)

Query: 79  YDLSDSVIVVYFNITYPGLS-MAIRKA 104
           Y + D V  VY N T PGLS  A+RKA
Sbjct: 260 YFIPDGVGFVYVNNTKPGLSDPAVRKA 286


>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
           X-Ray Crystallography. V93q Polymerase Variant
          Length = 773

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 18  ARSLERILEEAHLSGELNLSGRKLKDFPNSGGKYDLSDSVIVVYFSRSGRKLKDFPNSG 76
           AR LE IL+     G++  + R +K+      KY++    +V+Y  +  R LKD+  +G
Sbjct: 624 ARVLEAILKH----GDVEEAVRIVKEVTEKLSKYEVPPEKLVIY-EQITRDLKDYKATG 677


>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
           X-Ray Crystallography
          Length = 773

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 18  ARSLERILEEAHLSGELNLSGRKLKDFPNSGGKYDLSDSVIVVYFSRSGRKLKDFPNSG 76
           AR LE IL+     G++  + R +K+      KY++    +V+Y  +  R LKD+  +G
Sbjct: 624 ARVLEAILKH----GDVEEAVRIVKEVTEKLSKYEVPPEKLVIY-EQITRDLKDYKATG 677


>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
           Gorgonarius
          Length = 773

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 18  ARSLERILEEAHLSGELNLSGRKLKDFPNSGGKYDLSDSVIVVYFSRSGRKLKDFPNSG 76
           AR LE IL+     G++  + R +K+      KY++    +V+Y  +  R LKD+  +G
Sbjct: 624 ARVLEAILKH----GDVEEAVRIVKEVTEKLSKYEVPPEKLVIY-EQITRDLKDYKATG 677


  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    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,290,523
Number of Sequences: 62578
Number of extensions: 127805
Number of successful extensions: 229
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 226
Number of HSP's gapped (non-prelim): 24
length of query: 109
length of database: 14,973,337
effective HSP length: 73
effective length of query: 36
effective length of database: 10,405,143
effective search space: 374585148
effective search space used: 374585148
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: 45 (21.9 bits)