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= 039554
         (189 letters)

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

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



>pdb|3CFZ|A Chain A, Crystal Structure Of M. Jannaschii Periplasmic Binding
           Protein ModaWTPA WITH BOUND TUNGSTATE
          Length = 292

 Score = 27.7 bits (60), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 22/54 (40%)

Query: 45  NGILFYVFSKILPGTTQLSFWRLDGVILTALLHAGPVDFLYYWLHRALHHHYLY 98
           NG    +  K L   T   F R     L A L AG  D+L+ +   A  HH  Y
Sbjct: 164 NGTYLILVPKELDVDTNKLFVRSKETDLLAPLEAGAFDYLFIYKSVANQHHLKY 217


>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
           Mutant
          Length = 774

 Score = 26.9 bits (58), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 13  YRTAKGSNRIVDKAIEFEQVERERNWDDQIIFNGILFYVFSKILPGTTQL 62
           Y   KGS RI D+AI F++ +  ++  D        +Y+ +++LP   ++
Sbjct: 701 YIVLKGSGRIGDRAIPFDEFDPTKHKYDA------EYYIENQVLPAVERI 744


>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
           Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
          Length = 774

 Score = 26.9 bits (58), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 13  YRTAKGSNRIVDKAIEFEQVERERNWDDQIIFNGILFYVFSKILPGTTQL 62
           Y   KGS RI D+AI F++ +  ++  D        +Y+ +++LP   ++
Sbjct: 701 YIVLKGSGRIGDRAIPFDEFDPTKHKYDA------EYYIENQVLPAVERI 744


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

 Score = 26.9 bits (58), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 13  YRTAKGSNRIVDKAIEFEQVERERNWDDQIIFNGILFYVFSKILPGTTQL 62
           Y   KGS RI D+AI F++ +  ++  D        +Y+ +++LP   ++
Sbjct: 701 YIVLKGSGRIGDRAIPFDEFDPAKHKYDA------EYYIENQVLPAVERI 744


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

 Score = 26.9 bits (58), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 13  YRTAKGSNRIVDKAIEFEQVERERNWDDQIIFNGILFYVFSKILPGTTQL 62
           Y   KGS RI D+AI F++ +  ++  D        +Y+ +++LP   ++
Sbjct: 701 YIVLKGSGRIGDRAIPFDEFDPAKHKYDA------EYYIENQVLPAVERI 744


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

 Score = 26.9 bits (58), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 13  YRTAKGSNRIVDKAIEFEQVERERNWDDQIIFNGILFYVFSKILPGTTQL 62
           Y   KGS RI D+AI F++ +  ++  D        +Y+ +++LP   ++
Sbjct: 701 YIVLKGSGRIGDRAIPFDEFDPAKHKYDA------EYYIENQVLPAVERI 744


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

 Score = 26.9 bits (58), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 13  YRTAKGSNRIVDKAIEFEQVERERNWDDQIIFNGILFYVFSKILPGTTQL 62
           Y   KGS RI D+AI F++ +  ++  D        +Y+ +++LP   ++
Sbjct: 701 YIVLKGSGRIGDRAIPFDEFDPAKHKYDA------EYYIENQVLPAVERI 744


  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
   0.328    0.142    0.460 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,993,214
Number of Sequences: 62578
Number of extensions: 238962
Number of successful extensions: 4157
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 4145
Number of HSP's gapped (non-prelim): 26
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)