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= 013689
         (438 letters)

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

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



>pdb|3L5Z|A Chain A, Crystal Structure Of Transcriptional Regulator, Gntr
           Family From Bacillus Cereus
 pdb|3L5Z|B Chain B, Crystal Structure Of Transcriptional Regulator, Gntr
           Family From Bacillus Cereus
          Length = 156

 Score = 30.4 bits (67), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 23/49 (46%)

Query: 101 VIPSSTAPVDSDEYRAYLKTKLDLACAAVALRTAPVKPEDKSSLIENQT 149
           VIP   A V  +   +Y++ KL L      +R   ++P+DK     N T
Sbjct: 62  VIPGVEASVLEESIYSYIQNKLGLKVGTSVVRVKGIRPDDKEKQFXNLT 110


>pdb|2Q2E|A Chain A, Crystal Structure Of The Topoisomerase Vi Holoenzyme From
           Methanosarcina Mazei
          Length = 369

 Score = 29.6 bits (65), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 346 NQFFHQAIPSISTPTPNHQSLDSSFPSNIQLPTVGNPQSDRGGKNMTETSPL---QHAVG 402
           NQF  + +PS+S P+    +L+ S  S++ +   G+ +S+R  K +     L    +A  
Sbjct: 29  NQFEEEVVPSVSLPSRTKANLEYSDESDVWV--YGDRESERSAKTVKGAFQLLKTTYATD 86

Query: 403 L---EHVPQGVGHRVSPPGAV-PGWD 424
               EH+ +  G  +     +  GWD
Sbjct: 87  FLINEHLARNRGSTLRELYYISEGWD 112


>pdb|3TWL|A Chain A, Crystal Structure Of Arabidopsis Thaliana Fpg
 pdb|3TWM|A Chain A, Crystal Structure Of Arabidopsis Thaliana Fpg
 pdb|3TWM|B Chain B, Crystal Structure Of Arabidopsis Thaliana Fpg
          Length = 310

 Score = 29.3 bits (64), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 297 KMAEETVKRVTGLNPLLLARSDVPGVGMPLVNVPLDASRNATHPMQPNPN------QFFH 350
           + AE   K+   + PLLL +  + G+G  + +  L  +R   HP+Q   +      +  H
Sbjct: 159 EFAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQAR--IHPLQTASSLSKEQCEALH 216

Query: 351 QAIPSISTPTPNHQSLDSSFPSN 373
            +I  +        +  S FPSN
Sbjct: 217 TSIKEVIEKAVEVDADSSQFPSN 239


>pdb|3TWK|A Chain A, Crystal Structure Of Arabidopsis Thaliana Fpg
 pdb|3TWK|B Chain B, Crystal Structure Of Arabidopsis Thaliana Fpg
          Length = 297

 Score = 29.3 bits (64), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 297 KMAEETVKRVTGLNPLLLARSDVPGVGMPLVNVPLDASRNATHPMQPNPN------QFFH 350
           + AE   K+   + PLLL +  + G+G  + +  L  +R   HP+Q   +      +  H
Sbjct: 159 EFAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQAR--IHPLQTASSLSKEQCEALH 216

Query: 351 QAIPSISTPTPNHQSLDSSFPSN 373
            +I  +        +  S FPSN
Sbjct: 217 TSIKEVIEKAVEVDADSSQFPSN 239


  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
   0.310    0.127    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,192,094
Number of Sequences: 62578
Number of extensions: 380376
Number of successful extensions: 712
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 710
Number of HSP's gapped (non-prelim): 6
length of query: 438
length of database: 14,973,337
effective HSP length: 102
effective length of query: 336
effective length of database: 8,590,381
effective search space: 2886368016
effective search space used: 2886368016
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)