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= 025238
         (255 letters)

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

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



>pdb|3PFI|A Chain A, 2.7 Angstrom Resolution Crystal Structure Of A Probable
           Holliday Junction Dna Helicase (Ruvb) From Campylobacter
           Jejuni Subsp. Jejuni Nctc 11168 In Complex With
           Adenosine-5'-Diphosphate
 pdb|3PFI|B Chain B, 2.7 Angstrom Resolution Crystal Structure Of A Probable
           Holliday Junction Dna Helicase (Ruvb) From Campylobacter
           Jejuni Subsp. Jejuni Nctc 11168 In Complex With
           Adenosine-5'-Diphosphate
          Length = 338

 Score = 30.4 bits (67), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 15/69 (21%)

Query: 175 IQEEKIFTEAHMSEALRAVGCKGPEPDLLLVYGPVRCHLGFPAWRIRYTEIVHMGRLKSM 234
           + +E+I TE   +EAL ++G                  LGF A  +RY E++   + K +
Sbjct: 236 VNDEEIITEKRANEALNSLGVN---------------ELGFDAXDLRYLELLTAAKQKPI 280

Query: 235 RYGSLLKAI 243
              S+  A+
Sbjct: 281 GLASIAAAL 289


>pdb|1VL6|A Chain A, Crystal Structure Of Nad-Dependent Malic Enzyme (Tm0542)
           From Thermotoga Maritima At 2.61 A Resolution
 pdb|1VL6|B Chain B, Crystal Structure Of Nad-Dependent Malic Enzyme (Tm0542)
           From Thermotoga Maritima At 2.61 A Resolution
 pdb|1VL6|C Chain C, Crystal Structure Of Nad-Dependent Malic Enzyme (Tm0542)
           From Thermotoga Maritima At 2.61 A Resolution
 pdb|1VL6|D Chain D, Crystal Structure Of Nad-Dependent Malic Enzyme (Tm0542)
           From Thermotoga Maritima At 2.61 A Resolution
          Length = 388

 Score = 27.3 bits (59), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 10/26 (38%), Positives = 20/26 (76%)

Query: 87  QLLQWLVDIGVKHVCLYDAEGILKKS 112
            ++++L+D+GVK+V   D +GIL ++
Sbjct: 206 NIVKFLLDLGVKNVVAVDRKGILNEN 231


>pdb|2HAE|A Chain A, Crystal Structure Of A Putative Malic Enzyme (Malate
           Oxidoreductase)
 pdb|2HAE|B Chain B, Crystal Structure Of A Putative Malic Enzyme (Malate
           Oxidoreductase)
 pdb|2HAE|C Chain C, Crystal Structure Of A Putative Malic Enzyme (Malate
           Oxidoreductase)
 pdb|2HAE|D Chain D, Crystal Structure Of A Putative Malic Enzyme (Malate
           Oxidoreductase)
          Length = 386

 Score = 27.3 bits (59), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 10/26 (38%), Positives = 20/26 (76%)

Query: 87  QLLQWLVDIGVKHVCLYDAEGILKKS 112
            ++++L+D+GVK+V   D +GIL ++
Sbjct: 196 NIVKFLLDLGVKNVVAVDRKGILNEN 221


  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
   0.324    0.139    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,120,383
Number of Sequences: 62578
Number of extensions: 272036
Number of successful extensions: 791
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 789
Number of HSP's gapped (non-prelim): 5
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)