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= 006913
         (626 letters)

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

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



>pdb|3HXJ|A Chain A, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
           From Methanococcus Maripaludis, Northeast Structural
           Genomics Consortium Target Mrr86
 pdb|3HXJ|B Chain B, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
           From Methanococcus Maripaludis, Northeast Structural
           Genomics Consortium Target Mrr86
 pdb|3HXJ|C Chain C, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
           From Methanococcus Maripaludis, Northeast Structural
           Genomics Consortium Target Mrr86
 pdb|3HXJ|D Chain D, Crystal Structure Of Pyrrolo-quinoline Quinone (pqq_dh)
           From Methanococcus Maripaludis, Northeast Structural
           Genomics Consortium Target Mrr86
          Length = 330

 Score = 31.6 bits (70), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)

Query: 37  FRLSKPLIGEDGKIYACS-EKTLFAFESNGTIAWSLDLDFTCNIGTAPVHGGTGEVY 92
           + +++P I EDG IY  S +  L+A   +GT  W         I ++PV G T  +Y
Sbjct: 215 WTVTRPAISEDGTIYVTSLDGHLYAINPDGTEKWRFKTG--KRIESSPVIGNTDTIY 269



 Score = 30.0 bits (66), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 41 KPLIGEDGKIYACSEKTLFAFESNGTIAWSLD 72
          +P IG+DG IY  S+K ++A   +GT  W  D
Sbjct: 64 RPSIGKDGTIYFGSDK-VYAINPDGTEKWRFD 94


>pdb|1LRW|A Chain A, Crystal Structure Of Methanol Dehydrogenase From P.
           Denitrificans
 pdb|1LRW|C Chain C, Crystal Structure Of Methanol Dehydrogenase From P.
           Denitrificans
          Length = 600

 Score = 30.4 bits (67), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 30/124 (24%), Positives = 47/124 (37%), Gaps = 16/124 (12%)

Query: 158 GQLLWSAGPVLDQLGYRQGCTKTDVDCYFTSVPVIDQCEGSIYISNTQGELYSLSAHSPY 217
           G++LW   P  +       C    V+      P  DQ +  I+ +   G + ++ A +  
Sbjct: 84  GKILWQNKPKQNPTARTVACCDV-VNRGLAYWPGDDQVKPLIFRTQLDGHIVAMDAETGE 142

Query: 218 FNWIQDLSSFDKAFTLT-----------PGNNGYLYVTIPVRALVLALDTSSGNILWHK- 265
             WI + S      TLT            G++G     + VR  V A D  SG + W   
Sbjct: 143 TRWIMENSDIKVGSTLTIAPYVIKDLVLVGSSG---AELGVRGYVTAYDVKSGEMRWRAF 199

Query: 266 SVGP 269
           + GP
Sbjct: 200 ATGP 203


>pdb|2V0V|A Chain A, Crystal Structure Of Rev-Erb Beta
 pdb|2V0V|B Chain B, Crystal Structure Of Rev-Erb Beta
 pdb|2V0V|C Chain C, Crystal Structure Of Rev-Erb Beta
 pdb|2V0V|D Chain D, Crystal Structure Of Rev-Erb Beta
          Length = 194

 Score = 30.0 bits (66), Expect = 4.3,   Method: Composition-based stats.
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 490 FPPVYDAKSRSYSFQGAKKESVTIFHTL 517
           F  ++DAK R+ +F G+KK SV   H++
Sbjct: 65  FASLFDAKERTVTFLGSKKYSVDDLHSM 92


>pdb|1KV9|A Chain A, Structure At 1.9 A Resolution Of A Quinohemoprotein
           Alcohol Dehydrogenase From Pseudomonas Putida Hk5
          Length = 668

 Score = 28.9 bits (63), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 29/127 (22%), Positives = 45/127 (35%), Gaps = 21/127 (16%)

Query: 149 RALFAFMTHGQLLWSAGPVLDQLGYRQGCTKTDVDCYFTSVPVIDQCEGSIYISNTQGEL 208
           R +      G+ LW   P + ++  R  C     D     V +       +Y+    G L
Sbjct: 77  RVIAVDAASGKELWRYDPEVAKVKARTSC----CDAVNRGVALWGD---KVYVGTLDGRL 129

Query: 209 YSLSAHSPYFNWIQDLSSFDKAFTLTP-----------GNNGYLYVTIPVRALVLALDTS 257
            +L A +    W Q  +   K +++T            GN G  Y    VR  V A D  
Sbjct: 130 IALDAKTGKAIWSQQTTDPAKPYSITGAPRVVKGKVIIGNGGAEYG---VRGFVSAYDAD 186

Query: 258 SGNILWH 264
           +G + W 
Sbjct: 187 TGKLAWR 193


  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
   0.318    0.133    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,101,891
Number of Sequences: 62578
Number of extensions: 558085
Number of successful extensions: 1181
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1163
Number of HSP's gapped (non-prelim): 19
length of query: 626
length of database: 14,973,337
effective HSP length: 105
effective length of query: 521
effective length of database: 8,402,647
effective search space: 4377779087
effective search space used: 4377779087
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)