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= 017770
         (366 letters)

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

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



>pdb|1OKB|A Chain A, Crystal Structure Of Uracil-Dna Glycosylase From Atlantic
           Cod (Gadus Morhua)
 pdb|1OKB|B Chain B, Crystal Structure Of Uracil-Dna Glycosylase From Atlantic
           Cod (Gadus Morhua)
          Length = 223

 Score = 33.9 bits (76), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 190 VEDVKAVLALKEYFDGRNEVSNL-LSLMKATVTRVDVAGMGDRVCVDLCSLMRPGEGLLV 248
           ++DVK V+  ++ + G N+   L  S+ K       +  +   +C D+     PG G L 
Sbjct: 53  IQDVKVVILGQDPYHGPNQAHGLCFSVQKPVPPPPSLVNIYKELCTDIDGFKHPGHGDLS 112

Query: 249 GSFARGLFLVHS 260
           G   +G+ L+++
Sbjct: 113 GWAKQGVLLLNA 124


>pdb|2YXL|A Chain A, Crystal Structure Of Ph0851
          Length = 450

 Score = 28.9 bits (63), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 287 PGGKTCYLSELKSGKEVIV---VDQKGRQR-TAVVGRVKIE-SRPLILVEAKALALAGHS 341
           PGGKT +L+EL   K  I    VD+   +R    V R+ I+  +PL+    KA  + G  
Sbjct: 270 PGGKTTHLAELMKNKGKIYAFDVDKMRMKRLKDFVKRMGIKIVKPLVKDARKAPEIIGEE 329

Query: 342 EPSLFLWFLVCTSSSLI 358
                L    CTSS  I
Sbjct: 330 VADKVLLDAPCTSSGTI 346


>pdb|3M6X|A Chain A, Multi-Site-Specific 16s Rrna Methyltransferase Rsmf From
           Thermus Thermophilus In Space Group P21212
          Length = 464

 Score = 28.1 bits (61), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 286 VPGGKTCYLSELKSGKEVIVVDQ-KGRQRTAVVGRVKIESRPLILVEAKALALA 338
            PGGKT +L+    GK +++ ++  G++   ++  V+    PL + +A   ALA
Sbjct: 111 APGGKTTHLAARXGGKGLLLANEVDGKRVRGLLENVERWGAPLAVTQAPPRALA 164


  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
   0.319    0.134    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,199,174
Number of Sequences: 62578
Number of extensions: 401287
Number of successful extensions: 1144
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1143
Number of HSP's gapped (non-prelim): 8
length of query: 366
length of database: 14,973,337
effective HSP length: 100
effective length of query: 266
effective length of database: 8,715,537
effective search space: 2318332842
effective search space used: 2318332842
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: 52 (24.6 bits)