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= 017478
         (371 letters)

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

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



>pdb|1IRZ|A Chain A, Solution Structure Of Arr10-B Belonging To The Garp
          Family Of Plant Myb-Related Dna Binding Motifs Of The
          Arabidopsis Response Regulators
          Length = 64

 Score = 58.2 bits (139), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 29/60 (48%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 30 TTDPKPRLRWTVELHERFVDAVTQLGGPDKATPKTIMRVMGVKGLTLYHLKSHLQKFRLG 89
          T   KPR+ WT ELH +F+ AV  LG  ++A PK I+ +M V  LT  ++ SHLQKFR+ 
Sbjct: 1  TAQKKPRVLWTHELHNKFLAAVDHLG-VERAVPKKILDLMNVDKLTRENVASHLQKFRVA 59


>pdb|2CSB|A Chain A, Crystal Structure Of Topoisomerase V From Methanopyrus
           Kandleri (61 Kda Fragment)
 pdb|2CSB|B Chain B, Crystal Structure Of Topoisomerase V From Methanopyrus
           Kandleri (61 Kda Fragment)
          Length = 519

 Score = 30.0 bits (66), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 13/91 (14%)

Query: 135 QMEVQRRLHEQLEVQRHLQLRIEAQGKYMQSILEKACQTLASGETVTPASFKGTIGNQAV 194
           + ++ RR  EQ  V+  L+L    Q +Y   I E     LA        +F G+I   A 
Sbjct: 282 KRDIXRRYLEQRIVECALKL----QDRY--GIREDVALCLAR-------AFDGSISXIAT 328

Query: 195 PDVGTMKDFCPPLNFSQFQDLNLYGGDQIDH 225
               T+KD CP L   + + +N      ID 
Sbjct: 329 TPYRTLKDVCPDLTLEEAKSVNRTLATLIDE 359


  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
   0.316    0.134    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,607,166
Number of Sequences: 62578
Number of extensions: 469465
Number of successful extensions: 908
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 906
Number of HSP's gapped (non-prelim): 5
length of query: 371
length of database: 14,973,337
effective HSP length: 100
effective length of query: 271
effective length of database: 8,715,537
effective search space: 2361910527
effective search space used: 2361910527
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)