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= 008032
         (580 letters)

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

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



>pdb|2W9M|A Chain A, Structure Of Family X Dna Polymerase From Deinococcus
           Radiodurans
 pdb|2W9M|B Chain B, Structure Of Family X Dna Polymerase From Deinococcus
           Radiodurans
          Length = 578

 Score = 31.2 bits (69), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 34/126 (26%), Positives = 52/126 (41%), Gaps = 13/126 (10%)

Query: 432 GIQSVDTLSSTPTGVETPDVIDL--RKQQRKEPERP-LYQVLEEKEERIAPGTLLGTTHT 488
           G+   D +  TPT       +DL  R  + +EPE   L+Q L +  E +  G L G  HT
Sbjct: 274 GLSRGDEVLPTPTEAVVFHALDLPFRPAEYREPEHDDLWQTLPDPAELVTVGDLRGMIHT 333

Query: 489 YVVNTGTQDKAGAKRVDLLRGQKTDRVDVTLQPEELEVMDNVLPAKYEEAREEEKLRSQR 548
           +     T    GA        ++     +TL  E L   D+   A Y      E+LR Q 
Sbjct: 334 H----STWSDGGASI------REMAEATLTLGHEFLGTADHSRAAYYANGLTIERLREQL 383

Query: 549 EDFSDM 554
           ++  ++
Sbjct: 384 KEIREL 389


>pdb|3Q72|A Chain A, Crystal Structure Of Rad G-Domain-Gtp Analog Complex
 pdb|3Q72|B Chain B, Crystal Structure Of Rad G-Domain-Gtp Analog Complex
 pdb|3Q7P|A Chain A, Crystal Structure Of Rad G-Domain-Gtp Analog Complex
 pdb|3Q7P|B Chain B, Crystal Structure Of Rad G-Domain-Gtp Analog Complex
 pdb|3Q7Q|A Chain A, Crystal Structure Of Rad G-Domain Q148a-Gtp Analog Complex
 pdb|3Q7Q|B Chain B, Crystal Structure Of Rad G-Domain Q148a-Gtp Analog Complex
          Length = 166

 Score = 31.2 bits (69), Expect = 1.6,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 460 KEPERPLYQVLEEKEERIAPGTLLGTTHTYVV-----NTGTQDKAGAKRVDLLRGQKTDR 514
           +E    +Y + E+   R  PG  +     YV+     + G+ +KA   RV L R ++TD 
Sbjct: 47  EEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDD 106

Query: 515 VDVTL 519
           V + L
Sbjct: 107 VPIIL 111


>pdb|2DPX|A Chain A, Crystal Structure Of Human Rad Gtpase
 pdb|2DPX|B Chain B, Crystal Structure Of Human Rad Gtpase
          Length = 174

 Score = 30.8 bits (68), Expect = 2.2,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 460 KEPERPLYQVLEEKEERIAPGTLLGTTHTYVV-----NTGTQDKAGAKRVDLLRGQKTDR 514
           +E    +Y + E+   R  PG  +     YV+     + G+ +KA   RV L R ++TD 
Sbjct: 52  EEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDD 111

Query: 515 VDVTL 519
           V + L
Sbjct: 112 VPIIL 116


>pdb|2GJS|A Chain A, The Crystal Structure Of Human Rrad In Complex With Gdp
 pdb|2GJS|B Chain B, The Crystal Structure Of Human Rrad In Complex With Gdp
          Length = 176

 Score = 30.8 bits (68), Expect = 2.3,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 460 KEPERPLYQVLEEKEERIAPGTLLGTTHTYVV-----NTGTQDKAGAKRVDLLRGQKTDR 514
           +E    +Y + E+   R  PG  +     YV+     + G+ +KA   RV L R ++TD 
Sbjct: 52  EEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDD 111

Query: 515 VDVTL 519
           V + L
Sbjct: 112 VPIIL 116


  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
   0.313    0.134    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,471,075
Number of Sequences: 62578
Number of extensions: 648220
Number of successful extensions: 1129
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1120
Number of HSP's gapped (non-prelim): 14
length of query: 580
length of database: 14,973,337
effective HSP length: 104
effective length of query: 476
effective length of database: 8,465,225
effective search space: 4029447100
effective search space used: 4029447100
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)