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= 046623
         (218 letters)

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

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



>pdb|3OFJ|A Chain A, Crystal Structure Of N-Methyltransferase Nods From
           Bradyrhizobium Japonicum Wm9
 pdb|3OFK|A Chain A, Crystal Structure Of N-Methyltransferase Nods From
           Bradyrhizobium Japonicum Wm9 In Complex With
           S-Adenosyl-L-Homocysteine (Sah)
 pdb|3OFK|B Chain B, Crystal Structure Of N-Methyltransferase Nods From
           Bradyrhizobium Japonicum Wm9 In Complex With
           S-Adenosyl-L-Homocysteine (Sah)
 pdb|3OFK|C Chain C, Crystal Structure Of N-Methyltransferase Nods From
           Bradyrhizobium Japonicum Wm9 In Complex With
           S-Adenosyl-L-Homocysteine (Sah)
 pdb|3OFK|D Chain D, Crystal Structure Of N-Methyltransferase Nods From
           Bradyrhizobium Japonicum Wm9 In Complex With
           S-Adenosyl-L-Homocysteine (Sah)
          Length = 216

 Score = 28.1 bits (61), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 10/35 (28%), Positives = 21/35 (60%)

Query: 109 LVWGSDDLSQLSELGEFDMVIMSDVFYDPEEMVGL 143
           + W + D+ Q S    FD++++++V Y  E+M  +
Sbjct: 99  ISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQM 133


>pdb|4DWE|A Chain A, Crystal Structure Of A Hypothetical Protein (Bacova_03992)
           From Bacteroides Ovatus Atcc 8483 At 2.01 A Resolution
          Length = 480

 Score = 27.7 bits (60), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 112 GSDDLSQLSELGEFDMVIMSDVFYDPEEMVGL 143
           G+  L    E G+ + V++   FYDP E  GL
Sbjct: 258 GATKLYPFQENGDIEQVVIERAFYDPPEGSGL 289


>pdb|1D1R|A Chain A, Nmr Solution Structure Of The Product Of The E. Coli Ycih
           Gene
          Length = 116

 Score = 27.3 bits (59), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 129 IMSDVFYDPEEMVGLGKTLKRVCGTGRHTVVWAVSEVRTRTGDCLHELIMSQGFRV 184
           +++ V  D  E+  L   LK+ CG G   V   V E++    D L  L+ ++G +V
Sbjct: 49  LITGVDLDDAELTKLAAELKKKCGCG-GAVKDGVIEIQGDKRDLLKSLLEAKGMKV 103


  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
   0.321    0.138    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,988,292
Number of Sequences: 62578
Number of extensions: 212802
Number of successful extensions: 464
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: 461
Number of HSP's gapped (non-prelim): 6
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)