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= 039232
         (165 letters)

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

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



>pdb|3BSU|A Chain A, Hybrid-Binding Domain Of Human Rnase H1 In Complex With
           12- Mer RnaDNA
 pdb|3BSU|B Chain B, Hybrid-Binding Domain Of Human Rnase H1 In Complex With
           12- Mer RnaDNA
 pdb|3BSU|C Chain C, Hybrid-Binding Domain Of Human Rnase H1 In Complex With
           12- Mer RnaDNA
 pdb|3BSU|F Chain F, Hybrid-Binding Domain Of Human Rnase H1 In Complex With
           12- Mer RnaDNA
 pdb|3BSU|G Chain G, Hybrid-Binding Domain Of Human Rnase H1 In Complex With
           12- Mer RnaDNA
 pdb|3BSU|H Chain H, Hybrid-Binding Domain Of Human Rnase H1 In Complex With
           12- Mer RnaDNA
          Length = 53

 Score = 30.0 bits (66), Expect = 0.64,   Method: Composition-based stats.
 Identities = 11/27 (40%), Positives = 18/27 (66%)

Query: 83  GKDEFFVVRKGDLVGVYKSFTECQAQL 109
           G   F+ VR+G   GV+ ++ EC+AQ+
Sbjct: 1   GSHMFYAVRRGRKTGVFLTWNECRAQV 27


>pdb|1YZF|A Chain A, Crystal Structure Of The LipaseACYLHYDROLASE FROM
           ENTEROCOCCUS Faecalis
          Length = 195

 Score = 28.5 bits (62), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 100 KSFTECQAQLGSSICHPPVSVYKGNALPKGTEEYLASHGL--KNALYTIRAADLTEDLFG 157
           K   +   ++G++   P + +YK   +  GT+E+L + GL      Y +  A +  ++ G
Sbjct: 129 KELVKVAQEVGAAHNLPVIDLYKAMTVYPGTDEFLQADGLHFSQVGYELLGALIVREIKG 188

Query: 158 SLMP 161
            L P
Sbjct: 189 RLKP 192


>pdb|1QHK|A Chain A, N-Terminal Domain Of Saccharomyces Cerevisiae Rnase Hi
           Reveals A Fold With A Resemblance To The N-Terminal
           Domain Of Ribosomal Protein L9
          Length = 47

 Score = 28.1 bits (61), Expect = 2.2,   Method: Composition-based stats.
 Identities = 10/23 (43%), Positives = 16/23 (69%)

Query: 87  FFVVRKGDLVGVYKSFTECQAQL 109
           F+ VRKG   G+Y ++ EC+ Q+
Sbjct: 3   FYAVRKGRETGIYNTWNECKNQV 25


>pdb|3CAX|A Chain A, Crystal Structure Of Uncharacterized Protein Pf0695
          Length = 369

 Score = 27.3 bits (59), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)

Query: 100 KSFTECQAQLGSSI--CHPPVSVYKGNALPKGTEE 132
           + FT   + LG  +  CHPP SVY  N + K  +E
Sbjct: 269 RIFTRTPSVLGRPVQLCHPPKSVYVVNKILKAFKE 303


>pdb|2VL9|A Chain A, Oxidized Form Of Human Peroxiredoxin 5
 pdb|2VL9|B Chain B, Oxidized Form Of Human Peroxiredoxin 5
 pdb|2VL9|C Chain C, Oxidized Form Of Human Peroxiredoxin 5
 pdb|2VL9|D Chain D, Oxidized Form Of Human Peroxiredoxin 5
          Length = 173

 Score = 27.3 bits (59), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 69  PRSRKLKTEPQMKQGKDEFFVVRKGDLVGVYKSFTECQAQLGSSICHPPVSVYKGNALPK 128
           P     + EP  K    E F  +KG L GV  +FT      G S  H P  V +  AL  
Sbjct: 22  PAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTP-----GCSKTHLPGFVEQAEALKA 76

Query: 129 GTEEYLASHGLKNALYT 145
              + +AS  + +A  T
Sbjct: 77  KGVQVVASLSVNDAFVT 93


>pdb|1URM|A Chain A, Human Peroxiredoxin 5, C47s Mutant
          Length = 172

 Score = 26.9 bits (58), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 69  PRSRKLKTEPQMKQGKDEFFVVRKGDLVGVYKSFTECQAQLGSSICHPPVSVYKGNALPK 128
           P     + EP  K    E F  +KG L GV  +FT      GSS  H P  V +  AL  
Sbjct: 21  PAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTP-----GSSKTHLPGFVEQAEALKA 75

Query: 129 GTEEYLASHGLKNALYT 145
              + +A   + +A  T
Sbjct: 76  KGVQVVACLSVNDAFVT 92


  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    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,848,475
Number of Sequences: 62578
Number of extensions: 183223
Number of successful extensions: 462
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 460
Number of HSP's gapped (non-prelim): 6
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
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: 47 (22.7 bits)