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= 028009
         (215 letters)

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

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



>pdb|2VFR|A Chain A, Alditol Oxidase From Streptomyces Coelicolor A3(2): Native
           Enzyme
 pdb|2VFS|A Chain A, Alditol Oxidase From Streptomyces Coelicolor A3(2):
           Complex With Xylitol
 pdb|2VFT|A Chain A, Alditol Oxidase From Streptomyces Coelicolor A3(2):
           Complex With Sorbitol
 pdb|2VFU|A Chain A, Alditol Oxidase From Streptomyces Coelicolor A3(2):
           Complex With Mannitol
 pdb|2VFV|A Chain A, Alditol Oxidase From Streptomyces Coelicolor A3(2):
           Complex With Sulphite
          Length = 422

 Score = 32.3 bits (72), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 50/119 (42%), Gaps = 17/119 (14%)

Query: 65  TDHPGIDFTVTSPAGNVVHTVKGTSG----DKFEFKAP---RSGMYKFCFNNPYSTPETV 117
           TD P   F   +PA   +H V G       ++F    P   R   ++  F  P S  E  
Sbjct: 234 TDRPLDGFPYAAPAAEKMHPVPGMPAVNCTEQFGVPGPWHERLPHFRAEF-TPSSGAELQ 292

Query: 118 SFYIHVGHIPNEHNLAKDEHLDPINVKIAELREALE--SVVSEQKYLR---ARDTRHRH 171
           S Y+    +P EH LA    +D I   +A + +  E  +V ++ ++L     RDT   H
Sbjct: 293 SEYL----MPREHALAALHAMDAIRETLAPVLQTCEIRTVAADAQWLSPAYGRDTVAAH 347


>pdb|3H4Q|A Chain A, Crystal Structure Of Putative Acetyltransferase
           (Np_371943.1) From Staphylococcus Aureus Mu50 At 2.50 A
           Resolution
          Length = 188

 Score = 31.6 bits (70), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 9/75 (12%)

Query: 35  DVECVYEYVIYEGDTVAGNFVVVDHD-IFWSTDHPGIDFTVTSPAGNVVHTVKGTSGDKF 93
           D+   Y YV+ E D + G F+VVD D   W  D   ID+ V      V+H + G+     
Sbjct: 64  DIAKDYLYVLEENDKIYG-FIVVDQDQAEWYDD---IDWPVNREGAFVIHRLTGSK---- 115

Query: 94  EFKAPRSGMYKFCFN 108
           E+K   + ++ +  +
Sbjct: 116 EYKGAATELFNYVID 130


>pdb|2Y4O|A Chain A, Crystal Structure Of Paak2 In Complex With Phenylacetyl
           Adenylate
 pdb|2Y4O|B Chain B, Crystal Structure Of Paak2 In Complex With Phenylacetyl
           Adenylate
          Length = 443

 Score = 28.9 bits (63), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 6/62 (9%)

Query: 131 NLAKDEHLDPINVKIAELREALESVVSEQKYLRARDTRHRHTNESTRKRLLGYTIGEYVL 190
            L++D H+D +++ +    EA  SV   ++   AR+ +HR       K ++G + G  VL
Sbjct: 367 TLSRDGHMDRLDLAVELRSEAAASVTDGERAALARELQHRI------KTMVGVSSGVTVL 420

Query: 191 LA 192
            A
Sbjct: 421 AA 422


>pdb|1FIU|A Chain A, Tetrameric Restriction Endonuclease Ngomiv In Complex With
           Cleaved Dna
 pdb|1FIU|B Chain B, Tetrameric Restriction Endonuclease Ngomiv In Complex With
           Cleaved Dna
 pdb|1FIU|C Chain C, Tetrameric Restriction Endonuclease Ngomiv In Complex With
           Cleaved Dna
 pdb|1FIU|D Chain D, Tetrameric Restriction Endonuclease Ngomiv In Complex With
           Cleaved Dna
 pdb|4ABT|A Chain A, Crystal Structure Of Type Iif Restriction Endonuclease
           Ngomiv With Cognate Uncleaved Dna
 pdb|4ABT|B Chain B, Crystal Structure Of Type Iif Restriction Endonuclease
           Ngomiv With Cognate Uncleaved Dna
          Length = 286

 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 8/22 (36%), Positives = 17/22 (77%)

Query: 25  RLSSLSVTVNDVECVYEYVIYE 46
           R+SS+++   +++CVY + +YE
Sbjct: 227 RISSIALGTGEIDCVYHFALYE 248


>pdb|1JS8|A Chain A, Structure Of A Functional Unit From Octopus Hemocyanin
 pdb|1JS8|B Chain B, Structure Of A Functional Unit From Octopus Hemocyanin
          Length = 394

 Score = 26.6 bits (57), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 24/105 (22%), Positives = 45/105 (42%), Gaps = 19/105 (18%)

Query: 17  ALLMSLIGRLS--SLSVTVNDVECVYEYVIYEGDTVAGNFVVV--DHDIFWSTDHPGIDF 72
             L+  IG+ +  +  V   D EC          T  G F ++  +H++FW+ D     +
Sbjct: 296 GFLLRTIGQSADVNFDVCTKDGEC----------TFGGTFCILGGEHEMFWAFDRL-FKY 344

Query: 73  TVTSPAGNVVHTVKGTSGDKFEFKAPRSGMYKFCFNNPYSTPETV 117
            +T+     +  ++  + D F+ K    G+     +N Y +P TV
Sbjct: 345 DITTS----LKHLRLDAHDDFDIKVTIKGIDGHVLSNKYLSPPTV 385


  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
   0.321    0.135    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,232,065
Number of Sequences: 62578
Number of extensions: 258813
Number of successful extensions: 534
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 532
Number of HSP's gapped (non-prelim): 13
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
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)