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= 0002.0075.p
         (211 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...   222   2e-59

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

 Score =  222 bits (566), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 117/147 (79%), Positives = 125/147 (85%)

Query: 39  STPSTPATCNARARARARXIIDINMGCPVKKVCNSWCGSALLQNEKLVGRILDAVVNAVD 98
           + P   A C      R   IIDINMGCPVKKVCNSWCGSALLQ+E+LV RILDAVV+AVD
Sbjct: 74  ADPVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEELVARILDAVVSAVD 133

Query: 99  VPVTLKFRTGWNRENKNALAIAAMAEQSGIAMLTLHGRTRADGYSGEAEYETIAAVKAAV 158
           VPVTLKFRTGWNR NKNAL IAA AE +GIAMLTLHGRTRADGYSGEAEYETIAAVKAAV
Sbjct: 134 VPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGEAEYETIAAVKAAV 193

Query: 159 KIPVVANGDITTPERAKHVLTVTGADA 185
           KIPVVANGDITTPE+A+ VL +T ADA
Sbjct: 194 KIPVVANGDITTPEKARDVLLLTKADA 220


  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
   0.317    0.127    0.384 

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: 330,009
Number of extensions: 10444
Number of successful extensions: 55
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 55
Number of HSP's successfully gapped: 1
Length of query: 211
Length of database: 1,619,870
Length adjustment: 81
Effective length of query: 130
Effective length of database: 1,236,335
Effective search space: 160723550
Effective search space used: 160723550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 128 (53.9 bits)