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= psy9555
         (138 letters)

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

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



>pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli
 pdb|1KQG|A Chain A, Formate Dehydrogenase N From E. Coli
          Length = 1015

 Score = 29.3 bits (64), Expect = 0.65,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 27/59 (45%)

Query: 80  YDARIPEKWQKISWESATLGFWYTELLERDIQFRRWYQHGRPNVFWMTTRVTQNTYSSN 138
           Y A   +KWQ+ISWE A          +RD  F    + G     W++T +   + +SN
Sbjct: 113 YRAPGSDKWQRISWEEAFSRIAKLMKADRDANFIEKNEQGVTVNRWLSTGMLCASGASN 171


>pdb|3RN9|A Chain A, Structure Of The TolueneO-Xylene Monooxygenase Hydroxylase
           T201sL272E DOUBLE MUTANT
          Length = 498

 Score = 27.3 bits (59), Expect = 2.6,   Method: Composition-based stats.
 Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 16/89 (17%)

Query: 42  LKLAIDGTITGN-KFSSLICPSIQS--------------IVMSQGLKSSLDAMYDARIPE 86
           L LA D    G+  F+SLI  SIQ+              I++  G K     M D  I  
Sbjct: 206 LGLAADAAEAGDHTFASLI-SSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWR 264

Query: 87  KWQKISWESATLGFWYTELLERDIQFRRW 115
            W+  S E+  +  +YT L  R+  F+ +
Sbjct: 265 SWKLFSVETGPIMDYYTPLESRNQSFKEF 293


>pdb|1XR6|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase 3d From
           Human Rhinovirus Serotype 1b
          Length = 460

 Score = 26.9 bits (58), Expect = 3.4,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 19/28 (67%)

Query: 4   VREALQRMGALLPMNIFLRQEIDRIQRV 31
           ++EAL + G  LPM  FL+ E+ + +++
Sbjct: 141 LKEALDKYGVDLPMITFLKDELRKKEKI 168


>pdb|1J3M|A Chain A, Crystal Structure Of The Conserved Hypothetical Protein
          Tt1751 From Thermus Thermophilus Hb8
 pdb|1J3M|B Chain B, Crystal Structure Of The Conserved Hypothetical Protein
          Tt1751 From Thermus Thermophilus Hb8
          Length = 129

 Score = 25.8 bits (55), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 11/27 (40%), Positives = 18/27 (66%)

Query: 6  EALQRMGALLPMNIFLRQEIDRIQRVI 32
          EAL  +G LLP N+ LR+  + ++ +I
Sbjct: 67 EALPEIGLLLPCNVVLREAEEGVEVLI 93


  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    0.134    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,761,754
Number of Sequences: 62578
Number of extensions: 127951
Number of successful extensions: 523
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 520
Number of HSP's gapped (non-prelim): 5
length of query: 138
length of database: 14,973,337
effective HSP length: 89
effective length of query: 49
effective length of database: 9,403,895
effective search space: 460790855
effective search space used: 460790855
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)