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= 028344
         (210 letters)

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

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



>pdb|3H1T|A Chain A, The Fragment Structure Of A Putative Hsdr Subunit Of A
           Type I Restriction Enzyme From Vibrio Vulnificus Yj016
          Length = 590

 Score = 33.1 bits (74), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 78  CRRGPHPSNSNWTIALVCFVVSWFTFVIAFLLLLTGAALNDQHGEESMYFGN-YYCYVVK 136
           C RG    NSNW   L  F         AF +  T   L + + +   YFGN  Y Y ++
Sbjct: 311 CHRGSARDNSNWREILEYFEP-------AFQIGXTATPLREDNRDTYRYFGNPIYTYSLR 363

Query: 137 PGVFAG 142
            G+  G
Sbjct: 364 QGIDDG 369


>pdb|1IAX|A Chain A, Crystal Structure Of Acc Synthase Complexed With Plp
 pdb|1IAX|B Chain B, Crystal Structure Of Acc Synthase Complexed With Plp
 pdb|1IAY|A Chain A, Crystal Structure Of Acc Synthase Complexed With Cofactor
           Plp And Inhibitor Avg
          Length = 428

 Score = 28.1 bits (61), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 110 LLTGAALNDQHGEESMYFGNYYCYVVKP 137
           +L+  A N++HGE S YF  +  Y   P
Sbjct: 1   ILSKLATNEEHGENSPYFDGWKAYDSDP 28


>pdb|2BF6|A Chain A, Atomic Resolution Structure Of The Bacterial Sialidase
           Nani From Clostridium Perfringens In Complex With
           Alpha-Sialic Acid (Neu5ac)
          Length = 449

 Score = 27.7 bits (60), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 119 QHGEESMYFGNYYCYVVKPGVFAGGAVLSLASVTLGILY 157
           ++GE    F   Y  +VKPG +A   +  L++  +G+LY
Sbjct: 390 ENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLY 428


>pdb|2VK5|A Chain A, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
 pdb|2VK6|A Chain A, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
 pdb|2VK7|A Chain A, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
 pdb|2VK7|B Chain B, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
          Length = 452

 Score = 27.7 bits (60), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 119 QHGEESMYFGNYYCYVVKPGVFAGGAVLSLASVTLGILY 157
           ++GE    F   Y  +VKPG +A   +  L++  +G+LY
Sbjct: 390 ENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLY 428


>pdb|1UAN|A Chain A, Crystal Structure Of The Conserved Protein Tt1542 From
           Thermus Thermophilus Hb8
 pdb|1UAN|B Chain B, Crystal Structure Of The Conserved Protein Tt1542 From
           Thermus Thermophilus Hb8
          Length = 227

 Score = 27.7 bits (60), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 8/58 (13%)

Query: 81  GPHPSNSNWTIALVCFVVSWFTFVIAFLLLLTGAALNDQHGEESM--------YFGNY 130
           G HP   ++ + +  F+  W   V+A+    TG A ++  G + +        Y+GNY
Sbjct: 147 GNHPFAPSFLVKISAFIDQWEAAVLAYRSQFTGEAASETVGPKGVEARKAMRRYWGNY 204


  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    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,683,745
Number of Sequences: 62578
Number of extensions: 200886
Number of successful extensions: 381
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 378
Number of HSP's gapped (non-prelim): 6
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)