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= 003523
         (813 letters)

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

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



>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           Y436a Mutation In The Catalytic Site
 pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           Y436a Mutation In The Catalytic Site
          Length = 428

 Score = 32.3 bits (72), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 22/107 (20%), Positives = 47/107 (43%), Gaps = 1/107 (0%)

Query: 498 DAYINAIRRAKNFIYIENQYFIGSSYGWLSKDIRVEDINALQLIPKELSLKIVSKIEAGE 557
           ++Y+   R+ K  +  +        + W  K  R ED +   ++P  + LKI  ++    
Sbjct: 311 ESYLELYRKQKKHLNTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEP 370

Query: 558 DFRVYIVIPMWPEGVPESASVQAILGWQRRTIEMMYADVAQAIQKKG 604
              +    P+ P  V +  +   +L  Q R + ++ ++VA  ++K G
Sbjct: 371 QGIIACCNPV-PPLVRQQINEMHLLIQQAREMPLLKSEVAAGVKKSG 416


>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
 pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
 pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
 pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
           D313n Mutation In The Active Site
          Length = 428

 Score = 32.3 bits (72), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 22/107 (20%), Positives = 47/107 (43%), Gaps = 1/107 (0%)

Query: 498 DAYINAIRRAKNFIYIENQYFIGSSYGWLSKDIRVEDINALQLIPKELSLKIVSKIEAGE 557
           ++Y+   R+ K  +  +        + W  K  R ED +   ++P  + LKI  ++    
Sbjct: 311 ESYLELYRKQKKHLNTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEP 370

Query: 558 DFRVYIVIPMWPEGVPESASVQAILGWQRRTIEMMYADVAQAIQKKG 604
              +    P+ P  V +  +   +L  Q R + ++ ++VA  ++K G
Sbjct: 371 QGIIACCNPV-PPLVRQQINEMHLLIQQAREMPLLKSEVAAGVKKSG 416


  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
   0.321    0.138    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,437,908
Number of Sequences: 62578
Number of extensions: 1116952
Number of successful extensions: 1828
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1828
Number of HSP's gapped (non-prelim): 4
length of query: 813
length of database: 14,973,337
effective HSP length: 107
effective length of query: 706
effective length of database: 8,277,491
effective search space: 5843908646
effective search space used: 5843908646
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)