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= 047583
         (77 letters)

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

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



>pdb|3VN5|A Chain A, Crystal Structure Of Aquifex Aeolicus Rnase H3
          Length = 257

 Score = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 26/71 (36%), Gaps = 12/71 (16%)

Query: 11  LQNNAKNQCGV------------PKGHVAVYVGELEKKRFVVPISYLSPPPFVDLLKRAE 58
           L    K +CGV            P G   ++  E E+   V   S  +   F+  LK  E
Sbjct: 163 LIERVKEECGVSEVVVDKYQPSNPFGEDVIFETEAERNLAVAVASIFARYKFLQSLKEVE 222

Query: 59  EELGFHHPMGA 69
            ELG   P G 
Sbjct: 223 RELGIKIPKGT 233


>pdb|3RDW|A Chain A, Putative Arsenate Reductase From Yersinia Pestis
 pdb|3RDW|B Chain B, Putative Arsenate Reductase From Yersinia Pestis
          Length = 121

 Score = 25.4 bits (54), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 42 ISYLSPPPFVDLLKRAEEELGF 63
          + YL  PP VD LK   ++LGF
Sbjct: 35 VLYLETPPSVDKLKELLQQLGF 56


  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    0.139    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,454,347
Number of Sequences: 62578
Number of extensions: 86485
Number of successful extensions: 181
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 179
Number of HSP's gapped (non-prelim): 2
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)