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= psy4851
         (62 letters)

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

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



>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
          Length = 760

 Score = 52.0 bits (123), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 25/44 (56%), Positives = 27/44 (61%)

Query: 15  RYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLP 58
           +YP GHFVR LG I     E E LLLEHDV +  FS  VL  LP
Sbjct: 220 KYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLP 263


>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
           Complex Bound To Rna
          Length = 1003

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 25/44 (56%), Positives = 27/44 (61%)

Query: 15  RYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLP 58
           +YP GHFVR LG I     E E LLLEHDV +  FS  VL  LP
Sbjct: 463 KYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLP 506


>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
          Length = 977

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 25/44 (56%), Positives = 27/44 (61%)

Query: 15  RYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLP 58
           +YP GHFVR LG I     E E LLLEHDV +  FS  VL  LP
Sbjct: 437 KYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLP 480


>pdb|3G5B|A Chain A, The Structure Of Unc5b Cytoplasmic Domain
          Length = 405

 Score = 26.6 bits (57), Expect = 3.5,   Method: Composition-based stats.
 Identities = 12/44 (27%), Positives = 24/44 (54%)

Query: 19  GHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPW 62
           G+ V    P+  KD+ + + L  HD+PH+ +   +L+    +P+
Sbjct: 196 GYLVEEPKPLLFKDSYHNLRLSLHDIPHAHWRSKLLAKYQEIPF 239


>pdb|2ISM|A Chain A, Crystal Structure Of The Putative Oxidoreductase (Glucose
           Dehydrogenase) (Ttha0570) From Thermus Theromophilus Hb8
 pdb|2ISM|B Chain B, Crystal Structure Of The Putative Oxidoreductase (Glucose
           Dehydrogenase) (Ttha0570) From Thermus Theromophilus Hb8
          Length = 352

 Score = 26.2 bits (56), Expect = 4.7,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 22/49 (44%)

Query: 13  HMRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMP 61
           H R+PQ  +V A   + +    N+V+ L H         +VL  +P  P
Sbjct: 83  HPRFPQEPYVYAYRTVAEGGLRNQVVRLRHLGERGVLDRVVLDGIPARP 131


  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
   0.326    0.146    0.473 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,993,527
Number of Sequences: 62578
Number of extensions: 61193
Number of successful extensions: 161
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 156
Number of HSP's gapped (non-prelim): 6
length of query: 62
length of database: 14,973,337
effective HSP length: 33
effective length of query: 29
effective length of database: 12,908,263
effective search space: 374339627
effective search space used: 374339627
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)