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= psy12566
         (220 letters)

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

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



>pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain
 pdb|2E6M|A Chain A, Structure Of Mouse Werner Exonuclease Domain
          Length = 208

 Score = 30.8 bits (68), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 80  PNSIILVDTADKFASALQDFA-RLDHNSHLGLDTEWKPNLSGGSPPTLALLQI-ATRDRV 137
           P SI+    A   +   +D + RL     +G D EW P    G    +A++Q+  +  + 
Sbjct: 14  PGSIVYSYEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKC 73

Query: 138 YILDIITLSKLP 149
           Y+  I ++S  P
Sbjct: 74  YLFHISSMSVFP 85


>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
           Reveals An Interplay Between The Active Site And The
           Hrdc Domain
 pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
           Reveals An Interplay Between The Active Site And The
           Hrdc Domain; Protein In Complex With Mn
 pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
           Reveals An Interplay Between The Active Site And The
           Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
 pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
           Reveals An Interplay Between The Active Site And The
           Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
          Length = 410

 Score = 28.5 bits (62), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 16/98 (16%)

Query: 84  ILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDII 143
           I VDT+ +  S L+D   L +   + +D E     S      + L+QI+TR+R Y++D +
Sbjct: 88  IWVDTSTELESMLED---LKNTKEIAVDLEHHDYRSYYG--IVCLMQISTRERDYLVDTL 142

Query: 144 TLSKLPCYAQLCHDLELI--VFANDDLLKIGFNLMPDV 179
            L +         +L ++  VF N  ++K+      D+
Sbjct: 143 KLRE---------NLHILNEVFTNPSIVKVFHGAFMDI 171


>pdb|2FBT|A Chain A, Wrn Exonuclease
 pdb|2FBV|A Chain A, Wrn Exonuclease, Mn Complex
 pdb|2FBX|A Chain A, Wrn Exonuclease, Mg Complex
 pdb|2FBY|A Chain A, Wrn Exonuclease, Eu Complex
 pdb|2FC0|A Chain A, Wrn Exonuclease, Mn Dgmp Complex
          Length = 205

 Score = 28.1 bits (61), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 108 LGLDTEWKPNLSGGSPPTLALLQI-ATRDRVYILDIITLSKLP 149
           +G D EW P  + G    +AL+Q+  +  + Y+  + ++S  P
Sbjct: 48  VGFDMEWPPLYNRGKLGKVALIQLCVSESKCYLFHVSSMSVFP 90


  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
   0.320    0.137    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,809,115
Number of Sequences: 62578
Number of extensions: 275211
Number of successful extensions: 548
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 548
Number of HSP's gapped (non-prelim): 3
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)