BLASTP 2.2.18 [Mar-02-2008]


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= 0002.0078.p
         (117 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309754|ref|YP_003773846.1| tRNA-dihydrouridine synthase or...   198   9e-53

>gi|300309754|ref|YP_003773846.1| tRNA-dihydrouridine synthase or
           NifR3-like protein [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score =  198 bits (504), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 91/116 (78%), Positives = 103/116 (88%)

Query: 1   MIGRAAQGRPWIFREIDHFLRTGTHLPAPMVAEVQELMLEHLQAHYAFYGEYLGVRTARK 60
           M+GRAAQGRPWIFREIDHFLRTG HLPAP+V+EV++LM EHLQAHYAFYG+YLGVRTARK
Sbjct: 222 MVGRAAQGRPWIFREIDHFLRTGEHLPAPLVSEVEQLMDEHLQAHYAFYGDYLGVRTARK 281

Query: 61  HIGWYVRDLPEGEQFRQRMNRLEDTQLQWNAVRDFFESQAAYGERLQYGIAGEALA 116
           HIGWYVRDLP GEQFR+ MNR+ED   Q  AVR FF SQAA+GERLQYG+A + +A
Sbjct: 282 HIGWYVRDLPGGEQFRRSMNRIEDCAQQLQAVRQFFASQAAFGERLQYGLAVDEVA 337


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.325    0.139    0.435 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 393,323
Number of extensions: 15406
Number of successful extensions: 52
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 52
Number of HSP's successfully gapped: 1
Length of query: 117
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 43
Effective length of database: 1,269,480
Effective search space: 54587640
Effective search space used: 54587640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 124 (52.4 bits)