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= 005799
         (676 letters)

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

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



>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/101 (34%), Positives = 54/101 (53%), Gaps = 2/101 (1%)

Query: 111 ASFAKTLTQSDANNGGGFSVPRYCAETIFPRLDYTADPPVQTVVAKDVHGEIWKFRHIYR 170
           A F K +T SD        +P++ AE  FP            +  +DV+G++W+FR+ Y 
Sbjct: 12  ALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW 71

Query: 171 GTPRRHLLTTGWSTFVNQKKLVAGDSIVFLRA--QDGDLCV 209
            + + ++LT GWS FV +K L AGD + F R+  QD  L +
Sbjct: 72  NSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYI 112


>pdb|3BU7|A Chain A, Crystal Structure And Biochemical Characterization Of
           Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter
           Pomeroyi
 pdb|3BU7|B Chain B, Crystal Structure And Biochemical Characterization Of
           Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter
           Pomeroyi
          Length = 394

 Score = 31.6 bits (70), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query: 477 FDGILTSHTNSSENLSCLLTMGNSNQNLEKSENIKKHQ 514
           +DG++  +TN       +LTMG S Q L   E+ K H+
Sbjct: 274 YDGLILRYTNPQTGGHPMLTMGASMQMLRPGEHTKAHR 311


>pdb|4FZ2|A Chain A, Crystal Structure Of The Fourth Type Of Archaeal Trna
           Splicing Endonuclease From Candidatus Micrarchaeum
           Acidiphilum Arman-2
 pdb|4FZ2|B Chain B, Crystal Structure Of The Fourth Type Of Archaeal Trna
           Splicing Endonuclease From Candidatus Micrarchaeum
           Acidiphilum Arman-2
          Length = 395

 Score = 31.2 bits (69), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 13/90 (14%)

Query: 7   SIDPQLWHACAGSMVQIPPLNSTVFYFPQGHAEHSLG-----SVNFPSSSRIPPLIFCRV 61
           +ID +L+H   G  ++IP  NS  F          +G     ++   + SR   L+    
Sbjct: 298 AIDFELYHRRGGD-IEIPGKNSPRFGMLSLSENERIGGSELSAIINEAKSRKLELVIA-- 354

Query: 62  SSLKFLADSETDEVYAKIKLVPIPANEIDF 91
                +ADSET   Y K++ V +P +E ++
Sbjct: 355 -----IADSETSVTYYKVRRVDLPKSEYEY 379


>pdb|3BNK|A Chain A, X-Ray Crystal Structure Of Flavoredoxin From
           Methanosarcina Acetivorans
 pdb|3BNK|B Chain B, X-Ray Crystal Structure Of Flavoredoxin From
           Methanosarcina Acetivorans
          Length = 196

 Score = 31.2 bits (69), Expect = 2.1,   Method: Composition-based stats.
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 32  YFPQGHAEHSLGSVNFPSSSRIPPLIFCRVSSLKFLADSETDEV-YAKIKLVPI 84
           Y P+G AE+   SVNFP S  +    +C + S + +  S   EV Y ++K  P+
Sbjct: 56  YTPEGIAENGSFSVNFPYSGMVKKTDYCGLVSGEKVDKSGLFEVFYGELKTAPM 109


>pdb|1YEL|A Chain A, Structure Of The Hypothetical Arabidopsis Thaliana Protein
           At1g16640.1
          Length = 104

 Score = 30.4 bits (67), Expect = 3.0,   Method: Composition-based stats.
 Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 143 DYTADPPVQTVVAKDVHGEIWKFRHIYRGTPRRHLLTTGWSTFVNQKKLVAGDSIVFLRA 202
           +Y   P   TV   D  G  W  R   RG   +  LT GW  FV    L  G  + F+  
Sbjct: 32  EYFPAPFPITVDLLDYSGRSWTVRMKKRG--EKVFLTVGWENFVKDNNLEDGKYLQFIYD 89

Query: 203 QD 204
           +D
Sbjct: 90  RD 91


>pdb|2IJ3|A Chain A, Structure Of The A264h Mutant Of Cytochrome P450 Bm3
 pdb|2IJ3|B Chain B, Structure Of The A264h Mutant Of Cytochrome P450 Bm3
          Length = 470

 Score = 30.0 bits (66), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 8/52 (15%)

Query: 629 GIERSDMLSHVLYQDASGAIKRTG----DEPFRYHLLVFACHLHEITMSISS 676
           G +  D+L+H+L    +G    TG    DE  RY ++ F  H HE T  + S
Sbjct: 227 GEQSDDLLTHML----NGKDPETGEPLDDENIRYQIITFLIHGHETTSGLLS 274


  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    0.132    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,093,804
Number of Sequences: 62578
Number of extensions: 755690
Number of successful extensions: 1556
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1553
Number of HSP's gapped (non-prelim): 9
length of query: 676
length of database: 14,973,337
effective HSP length: 105
effective length of query: 571
effective length of database: 8,402,647
effective search space: 4797911437
effective search space used: 4797911437
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: 55 (25.8 bits)