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= 009398
         (535 letters)

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

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



>pdb|2OCX|A Chain A, Crystal Structure Of Se-Met Fucosyltransferase Nodz From
           Bradyrhizobium
          Length = 330

 Score = 33.9 bits (76), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 23/35 (65%)

Query: 140 RYVVWIARAGLGNRILSIASAFLYALLTNRVLLID 174
           R+V+   R G G+ + S+ASA+ YA  T R L+ID
Sbjct: 5   RFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVID 39


>pdb|2HHC|A Chain A, Crystal Structure Of Fucosyltransferase Nodz From
           Bradyrhizobium
 pdb|2HLH|A Chain A, Crystal Structure Of Fucosyltransferase Nodz From
           Bradyrhizobium
 pdb|3SIW|A Chain A, Crystal Structure Of Nodz Alpha-1,6-Fucosyltransferase
           Co-Crystallized With Gdp
 pdb|3SIX|A Chain A, Crystal Structure Of Nodz Alpha-1,6-Fucosyltransferase
           Soaked With Gdp-Fucose
          Length = 330

 Score = 33.9 bits (76), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 4/52 (7%)

Query: 140 RYVVWIARAGLGNRILSIASAFLYALLTNRVLLIDEEPEMANLFCE-PFPNA 190
           R+V+   R G G+ + S+ASA+ YA  T R L+ID      + + E PF NA
Sbjct: 5   RFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWR---GSCYVEQPFSNA 53


>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
          Length = 382

 Score = 30.8 bits (68), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 23/108 (21%)

Query: 302 GRYLFHPSNQVWKLITSYYKKYLADAEE-RVGIQIRIFHKNSSPFQQVMDQILSCTDKEK 360
           G +LF P   + +++   +  Y+ D E  R  + I +FH+  +   Q M  I  CT    
Sbjct: 275 GAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQMISI--CT---- 328

Query: 361 LLPQVDMGKSIVAPFGKGKSK---AVLITSLIPSYYEKMKNMYLKHPT 405
                       A  GK + +   A+L+  L   +YEKMK   L+H +
Sbjct: 329 -----------AALIGKEERELPPAILL--LYSGWYEKMKQRVLQHAS 363


  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    0.137    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,212,906
Number of Sequences: 62578
Number of extensions: 675429
Number of successful extensions: 1255
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1253
Number of HSP's gapped (non-prelim): 3
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)