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= 038653
         (437 letters)

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

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



>pdb|2BA1|A Chain A, Archaeal Exosome Core
 pdb|2BA1|B Chain B, Archaeal Exosome Core
 pdb|2BA1|C Chain C, Archaeal Exosome Core
 pdb|3M7N|A Chain A, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M7N|B Chain B, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M7N|C Chain C, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M85|A Chain A, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
 pdb|3M85|B Chain B, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
 pdb|3M85|C Chain C, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
          Length = 179

 Score = 29.6 bits (65), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 24/101 (23%), Positives = 45/101 (44%), Gaps = 26/101 (25%)

Query: 87  LFHATRGNVFLKQSVVE----DPVADPVSGEKVSGRISELRTTI---------------- 126
           LF A  G + +K  V +     P+ + V G+ V GR+ +LR +I                
Sbjct: 29  LFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPS 88

Query: 127 --DVGLVHRSNL----LQTIADQFEQWNLLMEKVIYRTLNM 161
              +G++H SN+    ++ I++     ++L  +VI   L +
Sbjct: 89  NRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIGDNLRL 129


>pdb|1DIO|A Chain A, Diol Dehydratase-Cyanocobalamin Complex From Klebsiella
           Oxytoca
 pdb|1DIO|L Chain L, Diol Dehydratase-Cyanocobalamin Complex From Klebsiella
           Oxytoca
 pdb|1EGM|A Chain A, Crystal Structure Of Diol Dehydratase-Cyanocobalamin
           Complex At 100k.
 pdb|1EGM|L Chain L, Crystal Structure Of Diol Dehydratase-Cyanocobalamin
           Complex At 100k.
 pdb|1EEX|A Chain A, Crystal Structure Of The Diol Dehydratase-
           Adeninylpentylcobalamin Complex From Klebsiella Oxytoca
 pdb|1EEX|L Chain L, Crystal Structure Of The Diol Dehydratase-
           Adeninylpentylcobalamin Complex From Klebsiella Oxytoca
 pdb|1EGV|A Chain A, Crystal Structure Of The Diol Dehydratase-
           Adeninylpentylcobalamin Complex From Klebsella Oxytoca
           Under The Illuminated Condition.
 pdb|1EGV|L Chain L, Crystal Structure Of The Diol Dehydratase-
           Adeninylpentylcobalamin Complex From Klebsella Oxytoca
           Under The Illuminated Condition.
 pdb|1IWB|A Chain A, Crystal Structure Of Diol Dehydratase
 pdb|1IWB|L Chain L, Crystal Structure Of Diol Dehydratase
 pdb|1UC4|A Chain A, Structure Of Diol Dehydratase Complexed With (S)-1,2-
           Propanediol
 pdb|1UC4|L Chain L, Structure Of Diol Dehydratase Complexed With (S)-1,2-
           Propanediol
 pdb|1UC5|A Chain A, Structure Of Diol Dehydratase Complexed With (r)-1,2-
           Propanediol
 pdb|1UC5|L Chain L, Structure Of Diol Dehydratase Complexed With (r)-1,2-
           Propanediol
 pdb|3AUJ|A Chain A, Structure Of Diol Dehydratase Complexed With Glycerol
 pdb|3AUJ|L Chain L, Structure Of Diol Dehydratase Complexed With Glycerol
          Length = 554

 Score = 28.5 bits (62), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 298 IYGHTCDSTTVGLIKVQPTYPFNVDPRWQMIFLNSLFGYLSILIIVKLCTGSQADL 353
           + GHTC + T+ +   +P +    D  W   FL S   Y S  + ++  +GS +++
Sbjct: 213 MLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLAS--SYASRGLKMRFTSGSGSEV 266


  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
   0.324    0.139    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,459,657
Number of Sequences: 62578
Number of extensions: 485211
Number of successful extensions: 837
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: 837
Number of HSP's gapped (non-prelim): 9
length of query: 437
length of database: 14,973,337
effective HSP length: 102
effective length of query: 335
effective length of database: 8,590,381
effective search space: 2877777635
effective search space used: 2877777635
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)