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= 025129
         (257 letters)

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

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



>pdb|3ZRH|A Chain A, Crystal Structure Of The Lys29, Lys33-Linkage-Specific
           Trabid Otu Deubiquitinase Domain Reveals An
           Ankyrin-Repeat Ubiquitin Binding Domain (Ankubd)
          Length = 454

 Score = 30.8 bits (68), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 138 SASKQISAAISPDQNTTAFKEVAIIRHPRVGEYAFGFITSTVT 180
            A+K I A + P+      +E+A   H R G++A  F+T  VT
Sbjct: 95  QAAKCIPAMVCPELTEQIRREIAASLHQRKGDFACYFLTDLVT 137


>pdb|1ORO|A Chain A, A Flexible Loop At The Dimer Interface Is A Part Of The
           Active Site Of The Adjacent Monomer Of Escherichia Coli
           Orotate Phosphoribosyltransferase
 pdb|1ORO|B Chain B, A Flexible Loop At The Dimer Interface Is A Part Of The
           Active Site Of The Adjacent Monomer Of Escherichia Coli
           Orotate Phosphoribosyltransferase
          Length = 213

 Score = 28.5 bits (62), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 203 GDIFLVSSKEIIRPNLSIREGIEIIVSGGMTMPQVISPIERVAR 246
           G + LV   ++I    +IRE +EII + G T+  V+  ++R  R
Sbjct: 118 GRVMLVD--DVITAGTAIRESMEIIQANGATLAGVLISLDRQER 159


  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
   0.323    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: 7,079,489
Number of Sequences: 62578
Number of extensions: 263248
Number of successful extensions: 553
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 552
Number of HSP's gapped (non-prelim): 3
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
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: 50 (23.9 bits)