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= 048299
         (459 letters)

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

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



>pdb|1JEQ|A Chain A, Crystal Structure Of The Ku Heterodimer
 pdb|1JEY|A Chain A, Crystal Structure Of The Ku Heterodimer Bound To Dna
          Length = 609

 Score = 32.0 bits (71), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 16/65 (24%), Positives = 29/65 (44%)

Query: 54  RVGGLMNSPPAIHMRQLLISCAELFSQADFSAAHRLISILSANSSPYGDSIERLVHQFIR 113
           R   +M       + ++L  CA LFS   F  +H+ I + +   +P+G+   +      +
Sbjct: 130 RFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTK 189

Query: 114 ALSLR 118
           A  LR
Sbjct: 190 AGDLR 194


>pdb|1GNL|A Chain A, Hybrid Cluster Protein From Desulfovibrio Desulfuricans
           X-Ray Structure At 1.25a Resolution Using Synchrotron
           Radiation At A Wavelength Of 0.933a
 pdb|1GNL|B Chain B, Hybrid Cluster Protein From Desulfovibrio Desulfuricans
           X-Ray Structure At 1.25a Resolution Using Synchrotron
           Radiation At A Wavelength Of 0.933a
 pdb|1OA0|A Chain A, Reduced Hybrid Cluster Protein From Desulfovibrio
           Desulfuricans X-Ray Structure At 1.25a Resolution
 pdb|1OA0|B Chain B, Reduced Hybrid Cluster Protein From Desulfovibrio
           Desulfuricans X-Ray Structure At 1.25a Resolution
 pdb|1UPX|A Chain A, The Crystal Structure Of The Hybrid Cluster Protein From
           Desulfovibrio Desulfuricans Containing Molecules In The
           Oxidized And Reduced States.
 pdb|1UPX|B Chain B, The Crystal Structure Of The Hybrid Cluster Protein From
           Desulfovibrio Desulfuricans Containing Molecules In The
           Oxidized And Reduced States
          Length = 544

 Score = 29.6 bits (65), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 299 LLKDHDTRDLRLFLHKIKALNPRVVTIAEREASHNHPLFLQRFVEAVDHYG 349
           L+  HD RDL + L + +     V T +E   +H +P F +++     +YG
Sbjct: 236 LISGHDLRDLEMLLKQTEGTGVDVYTHSEMLPAHYYPAF-KKYAHFKGNYG 285


>pdb|1GN9|A Chain A, Hybrid Cluster Protein From Desulfovibrio Desulfuricans
           Atcc 27774 X-Ray Structure At 2.6a Resolution Using
           Synchrotron Radiation At A Wavelength Of 1.722a
 pdb|1GN9|B Chain B, Hybrid Cluster Protein From Desulfovibrio Desulfuricans
           Atcc 27774 X-Ray Structure At 2.6a Resolution Using
           Synchrotron Radiation At A Wavelength Of 1.722a
          Length = 544

 Score = 29.6 bits (65), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 299 LLKDHDTRDLRLFLHKIKALNPRVVTIAEREASHNHPLFLQRFVEAVDHYG 349
           L+  HD RDL + L + +     V T +E   +H +P F +++     +YG
Sbjct: 236 LISGHDLRDLEMLLKQTEGTGVDVYTHSEMLPAHYYPAF-KKYAHFKGNYG 285


  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
   0.323    0.136    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,277,136
Number of Sequences: 62578
Number of extensions: 394761
Number of successful extensions: 931
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 930
Number of HSP's gapped (non-prelim): 6
length of query: 459
length of database: 14,973,337
effective HSP length: 102
effective length of query: 357
effective length of database: 8,590,381
effective search space: 3066766017
effective search space used: 3066766017
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)