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= 031133
         (165 letters)

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

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



>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
           Bound To Amppnp
          Length = 997

 Score = 27.3 bits (59), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 17/36 (47%)

Query: 20  KILEYKAPMKVQDVLAEFAGHAISDSFPEIRHLMPD 55
           K+   K P   Q ++ +F  H I     E+ HLM D
Sbjct: 758 KLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMSD 793


>pdb|4A4K|A Chain A, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
           Domain
 pdb|4A4K|C Chain C, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
           Domain
 pdb|4A4K|E Chain E, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
           Domain
 pdb|4A4K|G Chain G, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
           Domain
 pdb|4A4K|I Chain I, Crystal Structure Of The S. Cerevisiae Ski2 Insertion
           Domain
          Length = 256

 Score = 27.3 bits (59), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 17/36 (47%)

Query: 20  KILEYKAPMKVQDVLAEFAGHAISDSFPEIRHLMPD 55
           K+   K P   Q ++ +F  H I     E+ HLM D
Sbjct: 219 KLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMSD 254


>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
           From Pyrococcus Horikoshii
 pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
           From Pyrococcus Horikoshii Complexed With Rna-Analog
          Length = 651

 Score = 26.9 bits (58), Expect = 5.8,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 33/54 (61%), Gaps = 5/54 (9%)

Query: 5   LMLEEKVIKVMKTDGKILEYKAPMKVQDVLAEFAGHAISDSFPEIRHLMPDFKL 58
           ++L++  I++ +++G+   Y+ P  +++V+     H I+  + E+R + PD +L
Sbjct: 289 VLLQKDFIEIQQSNGQDPLYR-PRDIKEVIK----HTITLDYGEVRDISPDIRL 337


  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    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,881,636
Number of Sequences: 62578
Number of extensions: 182544
Number of successful extensions: 249
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 247
Number of HSP's gapped (non-prelim): 3
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
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: 47 (22.7 bits)