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= 038725
         (244 letters)

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

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



>pdb|2WDW|A Chain A, The Native Crystal Structure Of The Primary Hexose Oxidase
           ( Dbv29) In Antibiotic A40926 Biosynthesis
 pdb|2WDW|B Chain B, The Native Crystal Structure Of The Primary Hexose Oxidase
           ( Dbv29) In Antibiotic A40926 Biosynthesis
 pdb|2WDX|A Chain A, The Complexed Crystal Structure Of The Primary Hexose
           Oxidase (Dbv29) In Antibiotic A40926 Biosynthesis
 pdb|2WDX|B Chain B, The Complexed Crystal Structure Of The Primary Hexose
           Oxidase (Dbv29) In Antibiotic A40926 Biosynthesis
 pdb|2WDX|C Chain C, The Complexed Crystal Structure Of The Primary Hexose
           Oxidase (Dbv29) In Antibiotic A40926 Biosynthesis
 pdb|2WDX|D Chain D, The Complexed Crystal Structure Of The Primary Hexose
           Oxidase (Dbv29) In Antibiotic A40926 Biosynthesis
          Length = 523

 Score = 29.6 bits (65), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 9/70 (12%)

Query: 133 YGGKMATIHNGASV--QIFATLKLS-------PNKTKIHHVWNRGLYVQGYSPTIHPTTS 183
           YGGK+ T+   A+   Q  A LK++       P     H  W R LY   Y+ T      
Sbjct: 403 YGGKVNTVDPAATALPQRDAILKVNYITGWANPGNEAKHLTWVRKLYADVYAETGGVPVP 462

Query: 184 NDLSSIATID 193
           ND+S  A I+
Sbjct: 463 NDVSDGAYIN 472


>pdb|3UWL|A Chain A, Crystal Structure Of Enteroccocus Faecalis Thymidylate
           Synthase (efts) In Complex With 5-formyl
           Tetrahydrofolate
 pdb|3UWL|C Chain C, Crystal Structure Of Enteroccocus Faecalis Thymidylate
           Synthase (efts) In Complex With 5-formyl
           Tetrahydrofolate
          Length = 315

 Score = 28.1 bits (61), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 129 SATLYGGKMATIHNGASVQI--FATLKLSPNKTKIHHVWNRGLYVQGYSPTIHPT 181
            A LY   +  +    S ++  F TL L+P+K  +       + V+GY P  HPT
Sbjct: 256 DAHLYQNHVEQMQEQLSREVRSFPTLVLNPDKASVFDFDMEDIKVEGYDP--HPT 308


>pdb|2IPC|A Chain A, Crystal Structure Of The Translocation Atpase Seca From
           Thermus Thermophilus Reveals A Parallel, Head-To-Head
           Dimer
 pdb|2IPC|B Chain B, Crystal Structure Of The Translocation Atpase Seca From
           Thermus Thermophilus Reveals A Parallel, Head-To-Head
           Dimer
 pdb|2IPC|C Chain C, Crystal Structure Of The Translocation Atpase Seca From
           Thermus Thermophilus Reveals A Parallel, Head-To-Head
           Dimer
 pdb|2IPC|D Chain D, Crystal Structure Of The Translocation Atpase Seca From
           Thermus Thermophilus Reveals A Parallel, Head-To-Head
           Dimer
          Length = 997

 Score = 28.1 bits (61), Expect = 4.2,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 100 LLPYILDPTVKLQKSPLLSRPLDINLISSSATLYGGKMATIHNGASVQIFATLKLSPN 157
           LLP     T +  K  L  R  D+ LI   A L+ GK+A +  G    + ATL ++ N
Sbjct: 60  LLPMAFALTRESAKRYLGMRHFDVQLIGG-AVLHEGKIAEMKTGEGKTLVATLAVALN 116


>pdb|3UWL|B Chain B, Crystal Structure Of Enteroccocus Faecalis Thymidylate
           Synthase (efts) In Complex With 5-formyl
           Tetrahydrofolate
 pdb|3UWL|D Chain D, Crystal Structure Of Enteroccocus Faecalis Thymidylate
           Synthase (efts) In Complex With 5-formyl
           Tetrahydrofolate
          Length = 315

 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 129 SATLYGGKMATIHNGASVQI--FATLKLSPNKTKIHHVWNRGLYVQGYSPTIHPT 181
            A LY   +  +    S ++  F TL L+P+K  +       + V+GY P  HPT
Sbjct: 256 DAHLYQNHVEQMQEQLSREVRSFPTLVLNPDKASVFDFDMEDIKVEGYDP--HPT 308


  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    0.133    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,075,803
Number of Sequences: 62578
Number of extensions: 266346
Number of successful extensions: 508
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 508
Number of HSP's gapped (non-prelim): 4
length of query: 244
length of database: 14,973,337
effective HSP length: 96
effective length of query: 148
effective length of database: 8,965,849
effective search space: 1326945652
effective search space used: 1326945652
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: 50 (23.9 bits)