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= 027572
         (221 letters)

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

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



>pdb|2SFA|A Chain A, Serine Proteinase From Streptomyces Fradiae Atcc 14544
          Length = 191

 Score = 27.7 bits (60), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 12/72 (16%)

Query: 7   GITSHSHIPNGERRARLYDKMARDLDDHGAAFLKQGETSQSLLLSDIFTLKDGSVTPVHK 66
           G+  HS+    + R  LY+   RD+   G A++  G+T Q          + GS T +H 
Sbjct: 67  GLIRHSNASAADGRVYLYNGSYRDITGAGNAYV--GQTVQ----------RSGSTTGLHS 114

Query: 67  AANPPVRANVLY 78
                + A V Y
Sbjct: 115 GRVTGLNATVNY 126


>pdb|1H2A|S Chain S, Single Crystals Of Hydrogenase From Desulfovibrio Vulgaris
          Length = 317

 Score = 27.7 bits (60), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 24/49 (48%)

Query: 64  VHKAANPPVRANVLYLSPKYSVPISDAVKRIFSPHFDKVIWFQNSSLYH 112
           V +A   P R +V+YL        S++V R F P+ D +I    S  YH
Sbjct: 47  VARALMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYH 95


>pdb|3FRZ|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase In Complex
          With
          Length = 576

 Score = 26.9 bits (58), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 17 GERRARLYDKMARDLDDHGAAFLKQGETSQSLLLSDIFTLKDGS-VTPVHKA 67
          G+R+ ++     +DLDDH    LK+ +   S + + + ++++   +TP H A
Sbjct: 46 GQRQKKVTFDRLQDLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSA 97


  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
   0.322    0.136    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,279,155
Number of Sequences: 62578
Number of extensions: 226745
Number of successful extensions: 664
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 662
Number of HSP's gapped (non-prelim): 4
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
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: 49 (23.5 bits)