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= 047612
         (238 letters)

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

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



>pdb|3O66|A Chain A, Crystal Structure Of Glycine BetaineCARNITINECHOLINE ABC
           TRANSPORTER
 pdb|3O66|B Chain B, Crystal Structure Of Glycine BetaineCARNITINECHOLINE ABC
           TRANSPORTER
          Length = 282

 Score = 28.5 bits (62), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 89  FEQTFFWIAGFNPTLAFRVVNESVK 113
           F+QTFF   GF  T AF V  E+ K
Sbjct: 102 FDQTFFDSYGFANTYAFXVTKETAK 126


>pdb|3SHG|A Chain A, Vbht Fic Protein From Bartonella Schoenbuchensis In
           Complex With Vbha Antitoxin
          Length = 205

 Score = 28.1 bits (61), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 4/41 (9%)

Query: 153 IMELARRRGRLGEWEMTEGVEVTESNLRASLESLVANADML 193
           I +LAR  G   +W+  E  E+T    RAS+ES   N+D++
Sbjct: 150 IWQLAREAGYHIDWDRVERQEMT----RASIESYYGNSDLM 186


>pdb|1BBY|A Chain A, Dna-Binding Domain From Human Rap30, Nmr, Minimized
          Average
 pdb|2BBY|A Chain A, Dna-Binding Domain From Human Rap30, Nmr, 30 Structures
          Length = 69

 Score = 26.9 bits (58), Expect = 9.2,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 29 QEHLLDELISAQENHHQSRDEDLKELVKRVLAHYQQYYQEKSKVAQHNVFLLFAPTW 85
          ++H+LD L SA E H     +DL ++ K+ + + ++  +E   +   NV  +   TW
Sbjct: 6  KQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKE---IGVQNVKGIHKNTW 59


  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
   0.318    0.130    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,422,392
Number of Sequences: 62578
Number of extensions: 220288
Number of successful extensions: 828
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 826
Number of HSP's gapped (non-prelim): 10
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)